Ctla2a (cytotoxic T lymphocyte-associated protein 2 alpha) - Rat Genome Database

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Gene: Ctla2a (cytotoxic T lymphocyte-associated protein 2 alpha) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ctla2a
Name: cytotoxic T lymphocyte-associated protein 2 alpha
RGD ID: 1565540
Description:
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC498690; protein CTLA-2-alpha; RGD1565540; similar to ctla-2-beta protein (141 AA)
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8173,809,052 - 3,828,872 (+)NCBIGRCr8
mRatBN7.2173,803,844 - 3,805,729 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl173,803,831 - 3,823,111 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx173,823,384 - 3,825,269 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0175,365,020 - 5,366,905 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0173,819,822 - 3,821,707 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0174,169,696 - 4,194,700 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl174,169,838 - 4,171,723 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0176,397,804 - 6,418,087 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4179,489,385 - 9,491,270 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera173,932,662 - 3,934,547 (+)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Ctla2a
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:38
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000061422
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat


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 appendage
High
Medium 3 42 47 37 19 37 6 29 33 11
Low 1 10 4 4 8 11 68 6 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000061422   ⟹   ENSRNOP00000058141
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl173,803,844 - 3,805,729 (+)Ensembl
Rnor_6.0 Ensembl174,169,838 - 4,171,723 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096326   ⟹   ENSRNOP00000097527
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl173,803,831 - 3,823,111 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119963   ⟹   ENSRNOP00000085362
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl173,803,831 - 3,808,252 (+)Ensembl
RefSeq Acc Id: NM_001109115   ⟹   NP_001102585
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8173,809,456 - 3,811,341 (+)NCBI
mRatBN7.2173,803,844 - 3,805,729 (+)NCBI
Rnor_6.0174,169,838 - 4,171,723 (+)NCBI
Rnor_5.0176,397,804 - 6,418,087 (+)NCBI
RGSC_v3.4179,489,385 - 9,491,270 (+)RGD
Celera173,932,662 - 3,934,547 (+)RGD
Sequence:
RefSeq Acc Id: XM_063276680   ⟹   XP_063132750
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8173,809,052 - 3,828,872 (+)NCBI
RefSeq Acc Id: XM_063276681   ⟹   XP_063132751
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8173,809,052 - 3,811,339 (+)NCBI
RefSeq Acc Id: NP_001102585   ⟸   NM_001109115
- UniProtKB: D3ZHI6 (UniProtKB/TrEMBL),   A6KAE9 (UniProtKB/TrEMBL),   A6KAF1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058141   ⟸   ENSRNOT00000061422
RefSeq Acc Id: ENSRNOP00000085362   ⟸   ENSRNOT00000119963
RefSeq Acc Id: ENSRNOP00000097527   ⟸   ENSRNOT00000096326
RefSeq Acc Id: XP_063132750   ⟸   XM_063276680
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063132751   ⟸   XM_063276681
- Peptide Label: isoform X2
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHI6-F1-model_v2 AlphaFold D3ZHI6 1-113 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700270
Promoter ID:EPDNEW_R10793
Type:initiation region
Name:Ctla2a_1
Description:cytotoxic T lymphocyte-associated protein 2 alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0174,169,825 - 4,169,885EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565540 AgrOrtholog
BioCyc Gene G2FUF-10473 BioCyc
Ensembl Genes ENSRNOG00000039971 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061422 ENTREZGENE
  ENSRNOT00000061422.3 UniProtKB/TrEMBL
  ENSRNOT00000096326.1 UniProtKB/TrEMBL
  ENSRNOT00000119963.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.2250 UniProtKB/TrEMBL
InterPro Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Prot_inhib_I29 UniProtKB/TrEMBL
KEGG Report rno:498690 UniProtKB/TrEMBL
NCBI Gene 498690 ENTREZGENE
Pfam Inhibitor_I29 UniProtKB/TrEMBL
PhenoGen Ctla2a PhenoGen
RatGTEx ENSRNOG00000039971 RatGTEx
SMART Inhibitor_I29 UniProtKB/TrEMBL
Superfamily-SCOP SSF54001 UniProtKB/TrEMBL
UniProt A0A8I6A3W4_RAT UniProtKB/TrEMBL
  A0A8I6ANI3_RAT UniProtKB/TrEMBL
  A6KAE9 ENTREZGENE, UniProtKB/TrEMBL
  A6KAF1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZHI6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Ctla2a  cytotoxic T lymphocyte-associated protein 2 alpha  RGD1565540_predicted  similar to ctla-2-beta protein (141 AA) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565540_predicted  similar to ctla-2-beta protein (141 AA) (predicted)  LOC498690  similar to ctla-2-beta protein (141 AA)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498690  similar to ctla-2-beta protein (141 AA)      Symbol and Name status set to provisional 70820 PROVISIONAL