TRIM49D1 (tripartite motif containing 49D1) - Rat Genome Database

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Gene: TRIM49D1 (tripartite motif containing 49D1) Homo sapiens
Analyze
No known orthologs.
Symbol: TRIM49D1
Name: tripartite motif containing 49D1
RGD ID: 6483629
HGNC Page HGNC:43973
Description: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response and regulation of gene expression. Predicted to be active in cytoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: TRIM49D; TRIM49D1P; TRIM49D2; TRIM49D2P; TRIM49DP; tripartite motif containing 49D, pseudogene; tripartite motif containing 49D1, pseudogene; tripartite motif-containing protein 49D; tripartite motif-containing protein 49D1; tripartite motif-containing protein 49D2 pseudogene
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Related Pseudogenes: LOC387770   TRIM53CP  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381189,911,409 - 89,922,245 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1189,911,111 - 89,922,245 (-)EnsemblGRCh38hg38GRCh38
GRCh371189,644,577 - 89,655,413 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361189,284,225 - 89,293,224 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map11q14.3ENTREZGENE
HuRef1185,853,671 - 85,859,906 (+)NCBIHuRef
CHM1_11189,528,306 - 89,534,619 (-)NCBICHM1_1
T2T-CHM13v2.01189,831,356 - 89,840,458 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:16554811   PMID:21873635   PMID:22144910  


Genomics

Variants

.
Variants in TRIM49D1
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q14.1-22.3(chr11:78232836-106779420)x1 copy number loss See cases [RCV000052710] Chr11:78232836..106779420 [GRCh38]
Chr11:77943882..106650146 [GRCh37]
Chr11:77621530..106155356 [NCBI36]
Chr11:11q14.1-22.3		 pathogenic
GRCh38/hg38 11q14.1-22.2(chr11:85242847-102920097)x1 copy number loss See cases [RCV000052711] Chr11:85242847..102920097 [GRCh38]
Chr11:84953891..102738968 [GRCh37]
Chr11:84631539..102296037 [NCBI36]
Chr11:11q14.1-22.2		 pathogenic
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
GRCh38/hg38 11q13.5-22.1(chr11:75941754-98357960)x1 copy number loss See cases [RCV000133838] Chr11:75941754..98357960 [GRCh38]
Chr11:75652798..98228688 [GRCh37]
Chr11:75330446..97733898 [NCBI36]
Chr11:11q13.5-22.1		 pathogenic
GRCh38/hg38 11q14.3(chr11:89898811-89923744)x1 copy number loss See cases [RCV000134612] Chr11:89898811..89923744 [GRCh38]
Chr11:89631979..89656912 [GRCh37]
Chr11:89271627..89296560 [NCBI36]
Chr11:11q14.3		 benign
GRCh38/hg38 11q14.3(chr11:89650515-90084741)x1 copy number loss See cases [RCV000137458] Chr11:89650515..90084741 [GRCh38]
Chr11:89383683..89817909 [GRCh37]
Chr11:89023331..89457557 [NCBI36]
Chr11:11q14.3		 pathogenic|likely benign
GRCh38/hg38 11q14.3(chr11:89727372-89972044)x3 copy number gain See cases [RCV000139678] Chr11:89727372..89972044 [GRCh38]
Chr11:89460540..89705212 [GRCh37]
Chr11:89100188..89344860 [NCBI36]
Chr11:11q14.3		 likely benign
GRCh38/hg38 11q14.3(chr11:89425778-90689442)x1 copy number loss See cases [RCV000141934] Chr11:89425778..90689442 [GRCh38]
Chr11:89158946..90422610 [GRCh37]
Chr11:88798594..90062258 [NCBI36]
Chr11:11q14.3		 uncertain significance
GRCh37/hg19 11q14.1-21(chr11:80318996-96116221)x1 copy number loss See cases [RCV000446395] Chr11:80318996..96116221 [GRCh37]
Chr11:11q14.1-21		 pathogenic
GRCh37/hg19 11q14.3(chr11:89540275-89956475)x3 copy number gain See cases [RCV000448705] Chr11:89540275..89956475 [GRCh37]
Chr11:11q14.3		 benign
GRCh37/hg19 11q14.3(chr11:89514122-92745981)x1 copy number loss See cases [RCV000448827] Chr11:89514122..92745981 [GRCh37]
Chr11:11q14.3		 uncertain significance
GRCh37/hg19 11q14.2-14.3(chr11:87099219-91921385) copy number loss Abnormal esophagus morphology [RCV000416734] Chr11:87099219..91921385 [GRCh37]
Chr11:11q14.2-14.3		 likely benign
GRCh37/hg19 11q14.1-21(chr11:84924674-93574799)x1 copy number loss See cases [RCV000448436] Chr11:84924674..93574799 [GRCh37]
Chr11:11q14.1-21		 likely pathogenic
GRCh37/hg19 11q14.2-22.3(chr11:88152458-109414650)x1 copy number loss See cases [RCV000510457] Chr11:88152458..109414650 [GRCh37]
Chr11:11q14.2-22.3		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q13.4-23.3(chr11:71588805-116680918)x3 copy number gain not provided [RCV000683374] Chr11:71588805..116680918 [GRCh37]
Chr11:11q13.4-23.3		 pathogenic
GRCh37/hg19 11q14.1-14.3(chr11:81771852-90851187) copy number loss Intellectual disability [RCV000721939] Chr11:81771852..90851187 [GRCh37]
Chr11:11q14.1-14.3		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q14.1-23.2(chr11:80053454-113316236)x1 copy number loss not provided [RCV000737595] Chr11:80053454..113316236 [GRCh37]
Chr11:11q14.1-23.2		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q14.1-21(chr11:83179196-94716998)x3 copy number gain not provided [RCV000750120] Chr11:83179196..94716998 [GRCh37]
Chr11:11q14.1-21		 pathogenic
GRCh37/hg19 11q14.3(chr11:89062443-89762600)x3 copy number gain not provided [RCV001006431] Chr11:89062443..89762600 [GRCh37]
Chr11:11q14.3		 likely benign
Single allele deletion Neurodevelopmental disorder [RCV000787372] Chr11:89482692..90933956 [GRCh37]
Chr11:11q14.3		 uncertain significance
GRCh37/hg19 11q14.1-14.3(chr11:84830143-92029933)x3 copy number gain not provided [RCV001006426] Chr11:84830143..92029933 [GRCh37]
Chr11:11q14.1-14.3		 pathogenic
NM_001384911.1(TRIM49D1):c.1337T>A (p.Ile446Asn) single nucleotide variant not specified [RCV004684738] Chr11:89911609 [GRCh38]
Chr11:89644777 [GRCh37]
Chr11:11q14.3		 uncertain significance
GRCh37/hg19 11q14.1-23.3(chr11:85422071-118022671)x1 copy number loss not provided [RCV001832892] Chr11:85422071..118022671 [GRCh37]
Chr11:11q14.1-23.3		 uncertain significance
GRCh37/hg19 11q14.1-21(chr11:84924674-93574799) copy number loss not specified [RCV002052942] Chr11:84924674..93574799 [GRCh37]
Chr11:11q14.1-21		 likely pathogenic
GRCh37/hg19 11q14.1-21(chr11:80318996-96116221) copy number loss not specified [RCV002052941] Chr11:80318996..96116221 [GRCh37]
Chr11:11q14.1-21		 pathogenic
GRCh37/hg19 11q14.3(chr11:89514122-92745981) copy number loss not specified [RCV002052946] Chr11:89514122..92745981 [GRCh37]
Chr11:11q14.3		 uncertain significance
GRCh37/hg19 11q14.1-22.1(chr11:77855209-98002445) copy number loss not specified [RCV002052940] Chr11:77855209..98002445 [GRCh37]
Chr11:11q14.1-22.1		 pathogenic
GRCh37/hg19 11p13-q25(chr11:32799481-134938470)x3 copy number gain MISSED ABORTION [RCV002282973] Chr11:32799481..134938470 [GRCh37]
Chr11:11p13-q25		 pathogenic
GRCh37/hg19 11q14.3(chr11:89474818-89887082)x1 copy number loss not provided [RCV002474964] Chr11:89474818..89887082 [GRCh37]
Chr11:11q14.3		 uncertain significance
GRCh37/hg19 11q14.1-22.3(chr11:81478509-104667040)x1 copy number loss not provided [RCV002475722] Chr11:81478509..104667040 [GRCh37]
Chr11:11q14.1-22.3		 pathogenic
NM_001384911.1(TRIM49D1):c.1141G>C (p.Gly381Arg) single nucleotide variant not specified [RCV004164309] Chr11:89911805 [GRCh38]
Chr11:89644973 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.1004C>T (p.Thr335Ile) single nucleotide variant not specified [RCV004162764] Chr11:89911942 [GRCh38]
Chr11:89645110 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.862G>T (p.Asp288Tyr) single nucleotide variant not specified [RCV004162295] Chr11:89912084 [GRCh38]
Chr11:89645252 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.927T>G (p.Ile309Met) single nucleotide variant not provided [RCV004704887]|not specified [RCV004096714] Chr11:89912019 [GRCh38]
Chr11:89645187 [GRCh37]
Chr11:11q14.3		 likely benign
NM_001384911.1(TRIM49D1):c.1100A>G (p.Gln367Arg) single nucleotide variant not specified [RCV004268404] Chr11:89911846 [GRCh38]
Chr11:89645014 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.907C>T (p.Arg303Cys) single nucleotide variant not specified [RCV004250860] Chr11:89912039 [GRCh38]
Chr11:89645207 [GRCh37]
Chr11:11q14.3		 likely benign
GRCh37/hg19 11q14.3(chr11:89602560-90979365)x3 copy number gain not provided [RCV003484848] Chr11:89602560..90979365 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.892A>G (p.Ser298Gly) single nucleotide variant not specified [RCV004475947] Chr11:89912054 [GRCh38]
Chr11:89645222 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.1223A>T (p.His408Leu) single nucleotide variant not specified [RCV004475946] Chr11:89911723 [GRCh38]
Chr11:89644891 [GRCh37]
Chr11:11q14.3		 uncertain significance
NM_001384911.1(TRIM49D1):c.905G>A (p.Arg302Gln) single nucleotide variant not specified [RCV004475948] Chr11:89912041 [GRCh38]
Chr11:89645209 [GRCh37]
Chr11:11q14.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:126
Interacting mature miRNAs:126
Transcripts:ENST00000420869, ENST00000530311
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
597058422GWAS1154496_Hbasophil percentage of leukocytes QTL GWAS1154496 (human)2e-10basophil percentage of leukocytesblood basophil count to total leukocyte count ratio (CMO:0000368)118992136889921369Human
597057764GWAS1153838_Hbasophil count QTL GWAS1153838 (human)4e-31basophil quantity (VT:0002607)blood basophil count (CMO:0000034)118992136889921369Human
597057344GWAS1153418_Hbasophil count QTL GWAS1153418 (human)3e-20basophil quantity (VT:0002607)blood basophil count (CMO:0000034)118992136889921369Human
597344882GWAS1440956_Hbody mass index QTL GWAS1440956 (human)2e-09body mass indexbody mass index (BMI) (CMO:0000105)118992136889921369Human
597169014GWAS1265088_Hbasophil count QTL GWAS1265088 (human)4e-28basophil quantity (VT:0002607)blood basophil count (CMO:0000034)118992136889921369Human


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 10 10 13 87 11 11 2 7 2 11 31 32 82 1 35 8

Sequence


Ensembl Acc Id: ENST00000420869   ⟹   ENSP00000474678
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1189,911,409 - 89,922,245 (-)Ensembl
Ensembl Acc Id: ENST00000530311   ⟹   ENSP00000474850
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1189,911,111 - 89,921,767 (-)Ensembl
Ensembl Acc Id: ENST00000605881   ⟹   ENSP00000479562
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1189,911,407 - 89,920,428 (-)Ensembl
RefSeq Acc Id: NM_001206627   ⟹   NP_001193556
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381189,911,409 - 89,920,447 (-)NCBI
GRCh371189,644,640 - 89,650,878 (-)ENTREZGENE
HuRef1185,827,215 - 85,833,450 (-)NCBI
CHM1_11189,460,932 - 89,548,942 (+)NCBI
T2T-CHM13v2.01189,831,356 - 89,840,394 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001384911   ⟹   NP_001371840
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381189,911,409 - 89,922,245 (-)NCBI
T2T-CHM13v2.01189,831,356 - 89,840,458 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001193556   ⟸   NM_001206627
- UniProtKB: I1YAP9 (UniProtKB/Swiss-Prot),   C9J1S8 (UniProtKB/Swiss-Prot),   A0A087WVN7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000474850   ⟸   ENST00000530311
Ensembl Acc Id: ENSP00000479562   ⟸   ENST00000605881
Ensembl Acc Id: ENSP00000474678   ⟸   ENST00000420869
RefSeq Acc Id: NP_001371840   ⟸   NM_001384911
- UniProtKB: C9J1S8 (UniProtKB/Swiss-Prot),   I1YAP9 (UniProtKB/Swiss-Prot),   A0A087WVN7 (UniProtKB/TrEMBL)
Protein Domains
B box-type   B30.2/SPRY   RING-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-C9J1S8-F1-model_v2 AlphaFold C9J1S8 1-452 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:43973 AgrOrtholog
COSMIC TRIM49D1 COSMIC
Ensembl Genes ENSG00000223417 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000233802 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000420869 ENTREZGENE
  ENST00000420869.3 UniProtKB/Swiss-Prot
  ENST00000526396.3 UniProtKB/Swiss-Prot
  ENST00000530311 ENTREZGENE
  ENST00000530311.6 UniProtKB/Swiss-Prot
  ENST00000605881.5 UniProtKB/TrEMBL
  ENST00000623787.3 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.920 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000223417 GTEx
  ENSG00000233802 GTEx
HGNC ID HGNC:43973 ENTREZGENE
Human Proteome Map TRIM49D1 Human Proteome Map
InterPro B30.2/SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B30.2/SPRY_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Butyrophylin_SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPRY_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRIM/RBCC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_B-box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:399939 UniProtKB/Swiss-Prot
  hsa:729384 UniProtKB/Swiss-Prot
NCBI Gene TRIM49DP ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRIPARTITE MOTIF-CONTAINING PROTEIN 49D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-B_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C3HC4_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA166049104 PharmGKB
PRINTS BUTYPHLNCDUF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE B302_SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_BBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART BBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPRY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP B-box zinc-binding domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING/U-box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WVN7 ENTREZGENE, UniProtKB/TrEMBL
  C9J1S8 ENTREZGENE
  I1YAP9 ENTREZGENE
  TR49D_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary I1YAP9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-12 TRIM49D1  tripartite motif containing 49D1  TRIM49D1P  tripartite motif containing 49D1, pseudogene  Symbol and/or name change 5135510 APPROVED
2013-01-22 TRIM49D1P  tripartite motif containing 49D1, pseudogene  TRIM49DP  tripartite motif containing 49D, pseudogene  Symbol and/or name change 5135510 APPROVED