TMIGD3 (transmembrane and immunoglobulin domain containing 3) - Rat Genome Database

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Gene: TMIGD3 (transmembrane and immunoglobulin domain containing 3) Homo sapiens
Analyze
Symbol: TMIGD3
Name: transmembrane and immunoglobulin domain containing 3
RGD ID: 9590048
HGNC Page HGNC:51375
Description: Predicted to enable transmembrane signaling receptor activity. Involved in negative regulation of cell migration and negative regulation of cell population proliferation. Located in membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AD026; AD026 protein (AD026); transmembrane domain-containing protein TMIGD3
RGD Orthologs
Mouse
Rat
Dog
Pig
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381111,483,348 - 111,563,962 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1111,483,348 - 111,563,962 (-)EnsemblGRCh38hg38GRCh38
GRCh371112,025,970 - 112,106,584 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1p13.2NCBI
CHM1_11112,140,977 - 112,221,590 (-)NCBICHM1_1
T2T-CHM13v2.01111,498,030 - 111,578,832 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (HEP)
genetic disease  (IAGP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IDA,IEA)
plasma membrane  (IBA,IEA,TAS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Xiong Y, etal., Emerg Microbes Infect. 2020 Dec;9(1):761-770. doi: 10.1080/22221751.2020.1747363.
Additional References at PubMed
PMID:8399349   PMID:9164961   PMID:9380026   PMID:9837869   PMID:12477932   PMID:12975309   PMID:15489334   PMID:16710414   PMID:21873635   PMID:27886186  


Genomics

Comparative Map Data
TMIGD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381111,483,348 - 111,563,962 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1111,483,348 - 111,563,962 (-)EnsemblGRCh38hg38GRCh38
GRCh371112,025,970 - 112,106,584 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1p13.2NCBI
CHM1_11112,140,977 - 112,221,590 (-)NCBICHM1_1
T2T-CHM13v2.01111,498,030 - 111,578,832 (-)NCBIT2T-CHM13v2.0
Tmigd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393105,778,174 - 105,831,360 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3105,811,799 - 105,826,108 (+)EnsemblGRCm39 Ensembl
GRCm39 Ensembl3105,778,174 - 105,816,242 (+)EnsemblGRCm39 Ensembl
GRCm39 Ensembl3105,778,219 - 105,831,358 (+)EnsemblGRCm39 Ensembl
GRCm383105,870,858 - 105,924,044 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3105,904,483 - 105,918,792 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl3105,870,858 - 105,908,926 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl3105,870,903 - 105,924,042 (+)EnsemblGRCm38mm10GRCm38
MGSCv363105,998,963 - 106,052,092 (+)NCBIMGSCv36mm8
Celera3108,059,748 - 108,112,934 (+)NCBICelera
Cytogenetic Map3F2.2NCBI
Tmigd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82196,027,286 - 196,103,430 (+)NCBIGRCr8
mRatBN7.22193,338,950 - 193,415,107 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2193,338,950 - 193,415,105 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2200,933,404 - 201,009,584 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02198,829,211 - 198,905,343 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02193,646,168 - 193,722,310 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02208,478,373 - 208,557,356 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2208,323,882 - 208,557,356 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02227,900,017 - 227,978,209 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42201,107,970 - 201,186,359 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2186,040,322 - 186,117,254 (+)NCBICelera
Cytogenetic Map2q34NCBI
TMIGD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11763,904,582 - 63,907,044 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1763,418,171 - 63,420,460 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01765,076,072 - 65,078,361 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11763,811,019 - 63,813,306 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01763,869,840 - 63,872,128 (+)NCBIUNSW_CanFamBas_1.0
TMIGD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4108,854,357 - 108,873,925 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14108,814,405 - 108,871,101 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24118,996,431 - 119,053,021 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in TMIGD3
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_000677.3(ADORA3):c.567C>T (p.Pro189=) single nucleotide variant Malignant melanoma [RCV000059835] Chr1:111500340 [GRCh38]
Chr1:112042962 [GRCh37]
Chr1:111844485 [NCBI36]
Chr1:1p13.2		 not provided
GRCh38/hg38 1p21.1-13.2(chr1:105468292-112190626)x1 copy number loss See cases [RCV000142760] Chr1:105468292..112190626 [GRCh38]
Chr1:106010914..112733248 [GRCh37]
Chr1:105812437..112534771 [NCBI36]
Chr1:1p21.1-13.2		 pathogenic
GRCh38/hg38 1p21.1-12(chr1:104325484-119977655)x3 copy number gain See cases [RCV000142953] Chr1:104325484..119977655 [GRCh38]
Chr1:104868106..120471049 [GRCh37]
Chr1:104669629..120321801 [NCBI36]
Chr1:1p21.1-12		 pathogenic
GRCh38/hg38 1p21.2-13.2(chr1:101618097-111703028)x1 copy number loss See cases [RCV000053879] Chr1:101618097..111703028 [GRCh38]
Chr1:102083653..112245650 [GRCh37]
Chr1:101856241..112047173 [NCBI36]
Chr1:1p21.2-13.2		 pathogenic
GRCh38/hg38 1p13.3-12(chr1:109756630-118650204)x3 copy number gain See cases [RCV000051827] Chr1:109756630..118650204 [GRCh38]
Chr1:110299252..119192827 [GRCh37]
Chr1:110100775..118994350 [NCBI36]
Chr1:1p13.3-12		 pathogenic
NM_000677.3(ADORA3):c.-581G>A single nucleotide variant not provided [RCV001644083] Chr1:111503935 [GRCh38]
Chr1:112046557 [GRCh37]
Chr1:1p13.2		 benign
NM_020683.7(TMIGD3):c.854G>C (p.Arg285Pro) single nucleotide variant Inborn genetic diseases [RCV002738421] Chr1:111486604 [GRCh38]
Chr1:112029226 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_000677.4(ADORA3):c.617A>T (p.Asn206Ile) single nucleotide variant Inborn genetic diseases [RCV002757127] Chr1:111500290 [GRCh38]
Chr1:112042912 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_020683.7(TMIGD3):c.991C>G (p.Pro331Ala) single nucleotide variant Inborn genetic diseases [RCV002737607] Chr1:111483740 [GRCh38]
Chr1:112026362 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_020683.7(TMIGD3):c.451A>G (p.Ile151Val) single nucleotide variant Inborn genetic diseases [RCV002763484] Chr1:111490662 [GRCh38]
Chr1:112033284 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_000677.4(ADORA3):c.681G>T (p.Lys227Asn) single nucleotide variant Inborn genetic diseases [RCV002788732] Chr1:111500226 [GRCh38]
Chr1:112042848 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_020683.7(TMIGD3):c.715C>T (p.Arg239Trp) single nucleotide variant Inborn genetic diseases [RCV002802583] Chr1:111488767 [GRCh38]
Chr1:112031389 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_020683.7(TMIGD3):c.419T>C (p.Met140Thr) single nucleotide variant Inborn genetic diseases [RCV002679444] Chr1:111490694 [GRCh38]
Chr1:112033316 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_000677.4(ADORA3):c.566C>A (p.Pro189His) single nucleotide variant ADORA3-related condition [RCV003956783] Chr1:111500341 [GRCh38]
Chr1:112042963 [GRCh37]
Chr1:1p13.2		 uncertain significance
NM_000677.4(ADORA3):c.583G>A (p.Ala195Thr) single nucleotide variant ADORA3-related condition [RCV003897380] Chr1:111500324 [GRCh38]
Chr1:112042946 [GRCh37]
Chr1:1p13.2		 likely benign

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 renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component
High
Medium 32 319 102 13 364 10 94 8 424 48 422 85 4 120 20 1
Low 1982 2057 1254 455 908 339 2616 1017 2887 244 682 1103 116 1039 1702 1
Below cutoff 304 593 342 137 486 94 1402 1051 362 84 256 222 46 1 45 1000 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000369716   ⟹   ENSP00000358730
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1111,483,348 - 111,503,633 (-)Ensembl
RefSeq Acc Id: ENST00000369717   ⟹   ENSP00000358731
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1111,483,348 - 111,563,962 (-)Ensembl
RefSeq Acc Id: ENST00000442484
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1111,483,348 - 111,489,662 (-)Ensembl
RefSeq Acc Id: ENST00000443498   ⟹   ENSP00000398770
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1111,483,569 - 111,563,934 (-)Ensembl
RefSeq Acc Id: ENST00000463993
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1111,486,639 - 111,489,690 (-)Ensembl
RefSeq Acc Id: ENST00000472933   ⟹   ENSP00000488683
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1111,485,315 - 111,488,824 (-)Ensembl
RefSeq Acc Id: NM_001081976   ⟹   NP_001075445
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381111,483,348 - 111,563,962 (-)NCBI
CHM1_11112,140,977 - 112,221,590 (-)NCBI
T2T-CHM13v2.01111,498,030 - 111,578,832 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001302680   ⟹   NP_001289609
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381111,483,348 - 111,563,962 (-)NCBI
CHM1_11112,140,977 - 112,221,590 (-)NCBI
T2T-CHM13v2.01111,498,030 - 111,578,832 (-)NCBI
Sequence:
RefSeq Acc Id: NM_020683   ⟹   NP_065734
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381111,483,348 - 111,503,633 (-)NCBI
CHM1_11112,140,977 - 112,161,659 (-)NCBI
T2T-CHM13v2.01111,498,030 - 111,518,318 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001289609   ⟸   NM_001302680
- Peptide Label: isoform 4
- UniProtKB: Q5QNY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001075445   ⟸   NM_001081976
- Peptide Label: isoform 3
- UniProtKB: Q6P2N6 (UniProtKB/Swiss-Prot),   Q5QNY7 (UniProtKB/Swiss-Prot),   P0DMS9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_065734   ⟸   NM_020683
- Peptide Label: isoform 1
- UniProtKB: P0DMS9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000398770   ⟸   ENST00000443498
RefSeq Acc Id: ENSP00000488683   ⟸   ENST00000472933
RefSeq Acc Id: ENSP00000358730   ⟸   ENST00000369716
RefSeq Acc Id: ENSP00000358731   ⟸   ENST00000369717

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0DMS9-F1-model_v2 AlphaFold P0DMS9 1-266 view protein structure

Promoters
RGD ID:6856608
Promoter ID:EPDNEW_H1469
Type:initiation region
Name:TMIGD3_1
Description:transmembrane and immunoglobulin domain containing 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1474  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381111,489,724 - 111,489,784EPDNEW
RGD ID:6856618
Promoter ID:EPDNEW_H1474
Type:initiation region
Name:TMIGD3_2
Description:transmembrane and immunoglobulin domain containing 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1469  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381111,563,962 - 111,564,022EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:51375 AgrOrtholog
COSMIC TMIGD3 COSMIC
Ensembl Genes ENSG00000121933 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000369716 ENTREZGENE
  ENST00000369716.9 UniProtKB/Swiss-Prot
  ENST00000369717 ENTREZGENE
  ENST00000369717.8 UniProtKB/Swiss-Prot
  ENST00000443498 ENTREZGENE
  ENST00000443498.5 UniProtKB/TrEMBL
  ENST00000472933.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000121933 GTEx
HGNC ID HGNC:51375 ENTREZGENE
Human Proteome Map TMIGD3 Human Proteome Map
InterPro Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:57413 UniProtKB/Swiss-Prot
NCBI Gene TMIGD3 ENTREZGENE
PANTHER POLYMERIC-IMMUNOGLOBULIN RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN TMIGD3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA166123749 PharmGKB
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0J9YY46_HUMAN UniProtKB/TrEMBL
  P0DMS9 ENTREZGENE
  Q5QNY7 ENTREZGENE
  Q5QNY8 ENTREZGENE, UniProtKB/TrEMBL
  Q6P2N6 ENTREZGENE
  TMIG3_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A2A3P4 UniProtKB/Swiss-Prot
  P33765 UniProtKB/Swiss-Prot
  Q5QNY7 UniProtKB/Swiss-Prot
  Q6P2N6 UniProtKB/Swiss-Prot
  Q6UWU0 UniProtKB/Swiss-Prot
  Q9BYZ1 UniProtKB/Swiss-Prot