IMGT Repertoire (MHC)
IMGT MHC entry from gene to protein for Oncorhynchus mykiss MH2-DB2
IMGT gene name and definition
- IMGT gene name: Oncorhynchus mykiss MH2-DB2
- IMGT gene definition: major histocompatibility complex (MHC) class II beta chain
Chromosomal localization
- Locus name: MH2-DB2
- Chromosome: 17
- Chromosomal localization: 17p
Gene exon/intron organization
Number of alleles: 2
IMGT reference alleles
| IMGT allele names | Literature allele names | Gene functionality | Strain | IMGT reference sequences | ||
|---|---|---|---|---|---|---|
| Exons | Accession numbers | Molecule type | ||||
| Oncmyk MH2-DB2*01 | OnmyDBB*01 | F | Mt. Shasta | EX1-5 | AF115529 | cDNA |
| Oncmyk MH2-DB2*02 | OnmyDBB-B5 | F | ARO-F2 | EX1-4 | AF115531 | cDNA |
IMGT reference sequences (in FASTA format) for the allele(s): Oncmyk MH2-DB2*01 to Oncmyk MH2-DB2*02
- Nucleotide sequence in FASTA format with gaps according to the IMGT unique numbering
- Amino acid sequence in FASTA format with gaps according to the IMGT unique numbering
- Nucleotide sequence in FASTA format without gaps
- Amino acid sequence in FASTA format without gaps
Other sequences from the literature
Corresponding protein database accession numbers
| Allele names | Accession numbers | Number of coding nucleotides | Number of coding amino acids | |
|---|---|---|---|---|
| Nucleotide databases EMBL | Protein databases | |||
| Oncmyk MH2-DB2*01 | AF115529 | Q9TNW2 | 738pb | 246aa |
| Oncmyk MH2-DB2*02 | AF115531 | Q9TNW0 | 640pb | 213aa |
- (1) Partial (3' part of EX4 missing).
Genomic sequence
Coding region sequence
The coding region (CODING-REGION)
sequence starts from INIT-CODON
(or its encoded amino acid) to STOP-CODON
(not included).
The nucleotide sequence is extracted from cDNA (c) sequences and/or is
built by artificial exon joining from genomic DNA (g) sequences.
The amino acid sequence is the translation of the nucleotide sequence.
Oncmyk MH2-DB2*01: AF115529(c)
Coding region structure
Nucleotide sequence
1 atgtctaagt caattcgctt ctacatttgc ctagccgtgg cattatccac tctgtatgaa 61 acagatggat atgcctccga tgtggtgact cgatgtttat acagctctat tgatatgcat 121 ggtgcagagt tcatacagtc ttataccttt aataaggttg aacatctcag attcaacagc 181 actgtgggtg agtttgttgg atacactgag ctgggtctga agaatgcaaa gagattgaac 241 cgtggtcaag aggtggttca aatgcgagga gagctggagc gtctatgtaa gcctaacgct 301 gatatccact acagagccat actggacaag acagttgagc cccatgtcag actgagctca 361 gtgactcccc ccagtggcag acaccctgcc atgctgatgt gcagcgccta tgacttctac 421 cccaaaccaa tcagagtgac ctggctgagg gacggacgtg aggtgaaatc tgatgtgacc 481 tccactgagg agctggctaa cggggactgg tactaccaga tccactccca cctggagtac 541 acacccaagt ctggagagaa gatctcctgc atggtggagc acatcagcct cactgagccc 601 atgatgtatc actgggaccc gtccctgcct gaggctgaga ggaataagat agcgatcggg 661 gcatctggtc tggtgctggg aaccatctta gcattagcag gactgatcta ctacaagaag 721 aagtcttctg gggtgctcta g
Amino acid sequence
1 MSKSIRFYIC LAVALSTLYE TDGYASDVVT RCLYSSIDMH GAEFIQSYTF NKVEHLRFNS 61 TVGEFVGYTE LGLKNAKRLN RGQEVVQMRG ELERLCKPNA DIHYRAILDK TVEPHVRLSS 121 VTPPSGRHPA MLMCSAYDFY PKPIRVTWLR DGREVKSDVT STEELANGDW YYQIHSHLEY 181 TPKSGEKISC MVEHISLTEP MMYHWDPSLP EAERNKIAIG ASGLVLGTIL ALAGLIYYKK 241 KSSGVL*
Legend:
- Colors are according to IMGT Color menu for regions and domains
- Nucleotide and amino acid letters (in bold) in purple, green or blue are according to IMGT Color menu for splicing types.
IMGT links
IMGT Repertoire
- Correspondence between nomenclatures (MHC): Teleostei
- Chromosomal localization: Vertebrate species (table)
- Protein displays (MHC): G-DOMAIN, C-LIKE-DOMAIN
- Alignment of alleles:
- Strand and loop lengths (MHC): G-DOMAIN, C-LIKE-DOMAIN
- Collier de perles (MHC): C-LIKE-DOMAIN
IMGT Scientific chart
- Numbering: G-DOMAIN, C-LIKE-DOMAIN
- Sequence and 3D structure identification and description: Label definitions for IG, TR and MHC, Standardized keywords and labels for IG, TR, MHC, RPI and FPIA
- Nomenclature: IMGT description of mutations
IMGT Index
IMGT Education
- Tutorials: Présentation du complexe majeur d'histocompatibilité, La superfamille des immunoglobulines (IgSF), La superfamille du complexe majeur d'histocompatibilité (MhcSF), Comparaison des différences entre les CMH des mammifères et ceux des Eutelostei
IMGT databases
- IMGT/3Dstructure-DB:
External links
Genome databases
- Entrez Gene:
Sequence databases
- EMBL: many entries (tables above)
- GenBank: many entries (tables above)
- DDBJ: many entries (tables above)
- Swiss-Prot: many entries (tables above)
- TrEMBL: many entries (tables above)
- NCBI: many entries (tables above)
Structure databases
- PDB:
Last updated: Friday, 15-Jan-2010 17:12:57 CET
Authors: Elodie Gemrot and Marie-Paule Lefranc
Editor: Chantal Ginestoux
Contact: Marie-Paule Lefranc
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References to cite:
Lefranc, M.-P. et al.,
Nucleic Acids Research, 27, 209-212 (1999)
Cover of NAR;
Ruiz, M. et al.,
Nucleic Acids Research, 28, 219-221 (2000);
Lefranc, M.-P.,
Nucleic Acids Research, 29, 207-209 (2001);
Lefranc, M.-P.,
Nucleic Acids Res., 31, 307-310 (2003);
Lefranc, M.-P. et al.,
In Silico Biol., 5, 0006 (2004) [Epub],
5, 45-60 (2005);
Lefranc, M.-P. et al.,
Nucleic Acids Res., 33, D593-D597 (2005)
Full text;
Lefranc, M.-P. et al.,
Nucleic Acids Research 2009 37: D1006-D1012; doi:10.1093/nar/gkn838
Full text.
For any other use please contact Marie-Paule Lefranc
Marie-Paule.Lefranc@igh.cnrs.fr.
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