EMBL Data Library Research Articles

Sequence Analysis of Scaffold/Matrix Attachment Regions (S/MARs) From Human Embryonic Kidney and Chinese Hamster Ovary Cells

Binding of intergenic Scaffold/Matrix Attachment Regions (S/MARs) to nuclear matrix proteins is believed to poise adjacent genes for transcription by forming chromatin loops. Vector constructs containing Scaffold/Matrix Attachment Regions (S/MAR) flanking the gene of interest, therefore, are able to enhance recombinant protein expression in mammalian cells. We compared two methods that are based on buffers containing 2M NaCl and Lithium-3,5-diidosalicylate (LIS) to isolate S/MARs from HEK293 and CHO DG44 cell lines. Isolated S/MARs were sequenced using the Illumina HiSeq platform and mapped against CHO DG44 genome contigs and the human genome GRCh37.p13 respectively (Sequence raw data from this article have been deposited at the EMBL Data Libraries under Study ID PRJEB26090 (ERP108063)). The 2M NaCl method produced 16 million S/MAR consensus sequences which included nine million and seven million from HEK293 and CHO DG44 respectively. LIS method, on the other hand, generated thirteen million S/MAR consensus containing 8.4 million and 4.7 million from HEK293 and CHO DG44, respectively. In order to compare all sets of S/MAR consensus, BLASTN analyses were performed based on exact matches. The number of perfect matches between S/MAR sequences produced by both methods was quite low: 0.46% and 0.07% for HEK293 and CHO DG44 cells respectively, indicating that the two methods isolate different sets of S/MARs. Comparison between the two cell lines found six S/MARs in common, with average coverage of 82%, obtained by the 2M NaCl method, but none of these are intergenic. The LIS method gave 38 S/MARs with average coverage of 85%, common to both cell types; of these, 13 were intergenic. We hypothesize that S/MARs from HEK293 and CHO DG44 isolated using the LIS method have the potential to be universal vector expression elements that can overcome the problem of low production yield.

Nomenclature for factors of the HLA system, update April 2010

The following sequences have been submitted to the Nomenclature Committee since the February 2010 nomenclature update and, following agreed policy, have been assigned official allele designations (1). Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided (5). The IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update June 2010

The following sequences have been submitted to the Nomenclature Committee since the May 2010 nomenclature update and, following agreed policy, have been assigned official allele designations (1). Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting

Nomenclature for factors of the HLA system, update February 2010

The following sequences have been submitted to the Nomenclature Committee since the January 2010 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). Together with the new format HLA allele sequence name, the designation prior to April 2010 is also listed. Full details of the change to the HLA nomenclature format is given in the recent nomenclature report (1). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data-libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update December 2009

The following sequences have been submitted to the Nomenclature Committee since the November 2009 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank, Vega or DDBJ data libraries. Although accession numbers have been assigned by the data-libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. Table 1 New Sequences Table 2 Confirmatory Sequences Table 3 Recently Published Sequences All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the World Wide Web at: http://www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update March 2009

The following sequences have been submitted to the Nomenclature Committee since the February 2009 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Beloware listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank, Vega or DDBJ data libraries. Although accession numbers have been assigned by the data-libraries and most sequencesarealreadyavailable, there is still thepossibility that an author may not yet have allowed the sequence to be released; in such a case youwill have to contact the submitting author directly. Additional information pertaining to new sequences is often included in thepublicationsdescribing these alleles; a listing of recent publications that describe newHLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/imgt/hla.

Nomenclature for factors of the HLA system, update February 2009

The following sequences have been submitted to the Nomenclature Committee since the January 2009 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank, Vega or DDBJ data libraries. Although accession numbers have been assigned by the data-libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/imgt/hla.

Nomenclature for factors of the HLA system, update December 2008

The following sequences have been submitted to the Nomenclature Committee since the November 2008 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given, and these can be used to retrieve the sequence files from the EMBL, GenBank, Vega or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case, you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at www.ebi.ac.uk/imgt/hla The sequence previously named as DRB1*1171 has now been shown to be a correction of the DRB1*110201 allele sequence, as such the name DRB1*1171 has now been abandoned.

Nomenclature for factors of the HLA system, update September 2008

The following sequences have been submitted to the Nomenclature Committee since the August 2008 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles, a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at: www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update March 2008

The following sequences have been submitted to the Nomenclature Committee since the February 2008 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case, you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. The sequence known previously as Cw*060202 has now been extended in length and shown to contain further coding polymorphisms when compared with the Cw*060201 allele. The name Cw*060202 has now been abandoned and the allele renamed Cw*0617. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at www.ebi.ac.uk/imgt/hla.

Nomenclature for factors of the HLA system, update October 2007

The following sequences have been submitted to the Nomenclature Committee since the September 2007 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released, in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles, a listing of recent publications which describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at: www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update November 2007

The following sequences have been submitted to the Nomenclature Committee since the October 2007 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given, and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although

Nomenclature for factors of the HLA system, update April 2007

The following sequences have been submitted to the Nomenclature Committee since the March 2007 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given, and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although

Nomenclature for factors of the HLA system, update January 2007

The following sequences have been submitted to the Nomenclature Committee since the December 2006 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from either the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released, in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles, a listing of recent publications which describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at www.ebi.ac.uk/imgt/hla.

Nomenclature for factors of the HLA system, update October 2006

The following sequences have been submitted to the Nomenclature Committee since the September 2006 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released, in such a case you will have to contact the submitting author directly. Additional

GenBank

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage ().

Nomenclature for factors of the HLA system, update July 2006

The following sequences have been submitted to the Nomenclature Committee since the June 2006 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given, and these numbers can be used to retrieve the sequence files from the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case, you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at http://www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update March 2006

The following sequences have been submitted to the Nomenclature Committee since the February 2006 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given, and these can be used to retrieve the sequence files from either the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles, a listing of recent publications which describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the world wide web at http://www.ebi.ac.uk/imgt/hla

Nomenclature for factors of the HLA system, update October 2005

The following sequences have been submitted to the Nomenclature Committee since the September 2005 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given, and these can be used to retrieve the sequence files from either the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publicationsdescribing these alleles, a listingof recent publications which describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for factors of the HLA system via the IMGT/ HLA database using the sequence submission tool provided. The IMGT/HLA database may be accessed via the worldwide web at http://www.ebi.ac.uk/imgt/hla

Abc1: a new ABC transporter from the fission yeast Schizosaccharomyces pombe.

We have isolated the abc1 gene from the fission yeast Schizosaccharomyces pombe. Sequence analysis suggests that the Abc1 protein is a member of the ABC superfamily of transporters and is composed of two structurally homologous halves, each consisting of a hydrophobic region of six transmembrane domains and a hydrophilic region containing one ATP-binding site. The abc1 gene appears to be expressed under all growth conditions but gene disruption experiments indicate that it is not essential for growth. The sequence of the abc1 gene has been deposited in the EMBL data library under the Accession Number Y09354.