B2M (beta-2-microglobulin) - Rat Genome Database

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Pathways
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Gene: B2M (beta-2-microglobulin) Canis lupus familiaris
Analyze
Symbol: B2M
Name: beta-2-microglobulin
RGD ID: 12153573
Description: ENCODES a protein that exhibits identical protein binding (inferred); protein homodimerization activity (inferred); structural molecule activity (inferred); INVOLVED IN antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (ortholog); antimicrobial humoral immune response mediated by antimicrobial peptide (ortholog); cellular response to iron(III) ion (ortholog); PARTICIPATES IN interleukin-12 signaling pathway; ASSOCIATED WITH acute kidney failure (ortholog); AGAT deficiency (ortholog); Albuminuria (ortholog); FOUND IN extracellular space (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13011,331,574 - 11,337,991 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3011,331,569 - 11,337,997 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3011,388,144 - 11,392,829 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03011,468,141 - 11,474,563 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13011,375,114 - 11,379,792 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03011,497,731 - 11,502,419 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03011,616,856 - 11,621,737 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (ISO)
AGAT deficiency  (ISO)
Albuminuria  (ISO)
arteriosclerosis  (ISO)
arthritis  (ISO)
autoimmune disease  (ISO)
Bloom syndrome  (ISO)
carotid artery disease  (ISO)
cataract  (ISO)
colorectal cancer  (ISO)
Colorectal Neoplasms  (ISO)
diffuse large B-cell lymphoma  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
encephalomyelitis  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Autoimmune Encephalomyelitis  (ISO)
Experimental Liver Cirrhosis  (ISO)
familial visceral amyloidosis  (ISO)
gastric adenocarcinoma  (ISO)
genetic disease  (ISO)
head and neck squamous cell carcinoma  (ISO)
heart disease  (ISO)
hemochromatosis  (ISO)
hereditary spastic paraplegia 11  (ISO)
Hypergammaglobulinemia  (ISO)
hypertension  (ISO)
Hypoproteinemia  (ISO)
immunodeficiency 43  (ISO)
inflammatory bowel disease  (ISO)
kidney disease  (ISO)
Knee Osteoarthritis  (ISO)
lung adenocarcinoma  (ISO)
lung oat cell carcinoma  (ISO)
lung small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
lymphoproliferative syndrome  (ISO)
measles  (ISO)
melanoma  (ISO)
multiple myeloma  (ISO)
non-Hodgkin lymphoma  (ISO)
obesity  (ISO)
ovarian serous cystadenocarcinoma  (ISO)
Paraproteinemias  (ISO)
Parkinson's disease  (ISO)
peripheral artery disease  (ISO)
peripheral T-cell lymphoma  (ISO)
plasma cell neoplasm  (ISO)
Prostatic Neoplasms  (ISO)
proteinuria  (ISO)
pyelonephritis  (ISO)
skin melanoma  (ISO)
Spondylarthritis  (ISO)
Systemic Inflammatory Response Syndrome  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
ureteral obstruction  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amyloid fibril formation  (IEA)
antigen processing and presentation of endogenous peptide antigen via MHC class I  (IEA)
antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent  (IEA,ISO)
antigen processing and presentation of peptide antigen via MHC class I  (IEA)
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
cellular response to iron ion  (IEA)
cellular response to iron(III) ion  (IEA,ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to nicotine  (IEA)
immune response  (IEA)
innate immune response  (ISO)
intracellular iron ion homeostasis  (IEA)
iron ion transport  (IEA,ISO)
learning or memory  (IEA)
multicellular organismal-level iron ion homeostasis  (IEA,ISO)
negative regulation of epithelial cell proliferation  (IEA)
negative regulation of forebrain neuron differentiation  (IEA)
negative regulation of neurogenesis  (IEA)
negative regulation of neuron projection development  (IEA,ISO)
peptide antigen assembly with MHC class I protein complex  (IEA)
positive regulation of cellular senescence  (IEA)
positive regulation of receptor-mediated endocytosis  (IEA)
positive regulation of T cell cytokine production  (IEA)
positive regulation of T cell mediated cytotoxicity  (IEA,ISO)
protein homotetramerization  (IEA)
protein refolding  (IEA,ISO)
regulation of erythrocyte differentiation  (IEA,ISO)
regulation of iron ion transport  (IEA)
regulation of membrane depolarization  (ISO)
response to cadmium ion  (ISO)
response to molecule of bacterial origin  (IEA,ISO)
response to xenobiotic stimulus  (ISO)
sensory perception of smell  (IEA)
T cell differentiation in thymus  (IEA,ISO)
T cell mediated cytotoxicity  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:17523091   PMID:22301074   PMID:23584472   PMID:30032202  


Genomics

Comparative Map Data
B2M
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13011,331,574 - 11,337,991 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3011,331,569 - 11,337,997 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3011,388,144 - 11,392,829 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03011,468,141 - 11,474,563 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13011,375,114 - 11,379,792 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03011,497,731 - 11,502,419 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03011,616,856 - 11,621,737 (+)NCBIUU_Cfam_GSD_1.0
B2M
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381544,711,517 - 44,718,145 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1544,711,358 - 44,718,851 (+)EnsemblGRCh38hg38GRCh38
GRCh371545,003,715 - 45,010,343 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361542,790,977 - 42,797,649 (+)NCBINCBI36Build 36hg18NCBI36
Build 341542,790,976 - 42,797,649NCBI
Celera1521,893,442 - 21,900,114 (+)NCBICelera
Cytogenetic Map15q21.1NCBI
HuRef1521,827,296 - 21,833,968 (+)NCBIHuRef
CHM1_11545,121,781 - 45,128,453 (+)NCBICHM1_1
T2T-CHM13v2.01542,519,493 - 42,526,121 (+)NCBIT2T-CHM13v2.0
B2m
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392121,978,168 - 121,983,563 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2121,978,167 - 121,983,564 (+)EnsemblGRCm39 Ensembl
GRCm382122,147,687 - 122,153,082 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2122,147,686 - 122,153,083 (+)EnsemblGRCm38mm10GRCm38
MGSCv372121,973,423 - 121,978,818 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362121,839,128 - 121,844,523 (+)NCBIMGSCv36mm8
Celera2123,294,935 - 123,300,323 (+)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.55NCBI
B2m
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83129,549,236 - 129,555,354 (+)NCBIGRCr8
mRatBN7.23109,095,740 - 109,101,764 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3109,095,729 - 109,101,766 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3112,769,695 - 112,775,711 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03121,365,215 - 121,371,231 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03119,025,591 - 119,031,607 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03114,087,287 - 114,093,311 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3114,087,287 - 114,093,309 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03120,627,499 - 120,633,523 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43108,927,919 - 108,932,718 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13108,833,491 - 108,838,291 (+)NCBI
Celera3107,993,988 - 108,000,012 (+)NCBICelera
RH 3.4 Map3954.3RGD
Cytogenetic Map3q35NCBI
B2m
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541611,204,849 - 11,215,568 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541611,205,503 - 11,211,325 (+)NCBIChiLan1.0ChiLan1.0
B2M
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21633,960,617 - 33,967,276 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11538,122,948 - 38,129,633 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01523,668,108 - 23,674,791 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11541,836,321 - 41,842,991 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1541,836,345 - 41,842,991 (+)Ensemblpanpan1.1panPan2
B2m
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864089,798,404 - 89,807,593 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364717,646,373 - 7,655,778 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364717,646,504 - 7,655,656 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
B2M
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1126,835,143 - 126,981,582 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11126,837,721 - 126,844,043 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
B2M
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12638,331,818 - 38,338,785 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2638,331,442 - 38,338,809 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666048102,721,246 - 102,728,233 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
B2m
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480411,514,728 - 11,521,625 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in B2M
122 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High 5 21 6 6 6 6 6 10 6
Medium 5 1 6 6 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000038089   ⟹   ENSCAFP00000033760
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3011,331,771 - 11,337,997 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000068406   ⟹   ENSCAFP00000047956
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3011,331,569 - 11,337,505 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000076683   ⟹   ENSCAFP00000050244
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3011,331,771 - 11,337,997 (+)Ensembl
RefSeq Acc Id: NM_001284479   ⟹   NP_001271408
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13011,331,778 - 11,336,463 (+)NCBI
Dog10K_Boxer_Tasha3011,388,144 - 11,392,829 (+)NCBI
ROS_Cfam_1.03011,468,345 - 11,473,035 (+)NCBI
UMICH_Zoey_3.13011,375,114 - 11,379,792 (+)NCBI
UNSW_CanFamBas_1.03011,497,731 - 11,502,419 (+)NCBI
UU_Cfam_GSD_1.03011,616,856 - 11,621,737 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038441716   ⟹   XP_038297644
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03011,468,141 - 11,474,563 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001271408   ⟸   NM_001284479
- Peptide Label: precursor
- UniProtKB: E2RN10 (UniProtKB/TrEMBL),   A0A8C0LC59 (UniProtKB/TrEMBL),   A0A8C0NI65 (UniProtKB/TrEMBL),   A0A8C0NAW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000033760   ⟸   ENSCAFT00000038089
RefSeq Acc Id: ENSCAFP00000047956   ⟸   ENSCAFT00000068406
RefSeq Acc Id: ENSCAFP00000050244   ⟸   ENSCAFT00000076683
RefSeq Acc Id: XP_038297644   ⟸   XM_038441716
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LC59 (UniProtKB/TrEMBL),   A0A8C0NI65 (UniProtKB/TrEMBL),   E2RN10 (UniProtKB/TrEMBL),   A0A8C0NAW2 (UniProtKB/TrEMBL)
Protein Domains
Ig-like   Ig-like C1-type   Immunoglobulin C1-set

Promoters
RGD ID:13688506
Promoter ID:EPDNEW_C6574
Type:multiple initiation site
Name:B2M_1
Description:beta-2-microglobulin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13011,331,757 - 11,331,817EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000013633 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030014114 UniProtKB/TrEMBL
  ENSCAFG00040021878 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000038089.4 UniProtKB/TrEMBL
  ENSCAFT00030026170.1 UniProtKB/TrEMBL
  ENSCAFT00030026221.1 UniProtKB/TrEMBL
  ENSCAFT00030026267.1 UniProtKB/TrEMBL
  ENSCAFT00040040613.1 UniProtKB/TrEMBL
  ENSCAFT00040040693.1 UniProtKB/TrEMBL
  ENSCAFT00040040720.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro B2Microglobulin UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report cfa:100855741 UniProtKB/TrEMBL
NCBI Gene B2M ENTREZGENE
PANTHER MHC CLASS II-RELATED UniProtKB/TrEMBL
  PTHR19944:SF62 UniProtKB/TrEMBL
Pfam C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
  PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8C0LC59 ENTREZGENE
  A0A8C0NAW2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0NI65 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0TD81_CANLF UniProtKB/TrEMBL
  B2MG_CANLF UniProtKB/Swiss-Prot
  E2RN10 ENTREZGENE, UniProtKB/TrEMBL
  P19341 ENTREZGENE
VGNC ID VGNC:38331 ENTREZGENE