Cmtm2a (CKLF-like MARVEL transmembrane domain containing 2A) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Cmtm2a (CKLF-like MARVEL transmembrane domain containing 2A) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Cmtm2a
Name: CKLF-like MARVEL transmembrane domain containing 2A
RGD ID: 1307501
Description: Predicted to be active in membrane. Orthologous to human CMTM2 (CKLF like MARVEL transmembrane domain containing 2); INTERACTS WITH bisphenol A; ochratoxin A; testosterone enanthate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: chemokine-like factor super family 1; CKLF-like MARVEL transmembrane domain-containing protein 2A; Cklfsf1; LOC307616
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819678,154 - 685,274 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl19678,135 - 685,390 (+)EnsemblGRCr8
mRatBN7.219671,719 - 678,839 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19671,719 - 678,837 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx19667,469 - 674,643 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,434,271 - 1,441,445 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019709,482 - 716,657 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.019880,024 - 887,144 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19880,024 - 887,144 (+)Ensemblrn6Rnor6.0
Rnor_5.019878,307 - 885,427 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.419629,381 - 636,501 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera19667,618 - 674,738 (+)NCBICelera
RGSC_v3.119629,380 - 636,501 (+)NCBI
Cytogenetic Map19p14NCBI
JBrowse:




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

Cellular Component
membrane  (IBA,IEA)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:14576337   PMID:19398553   PMID:21351585   PMID:24594480   PMID:26003139  


Genomics

Variants

.
Variants in Cmtm2a
15 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:21
Interacting mature miRNAs:22
Transcripts:ENSRNOT00000061648
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131969901Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124694445Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127361636Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat

Markers in Region
BE113910  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219678,788 - 678,938 (+)MAPPERmRatBN7.2
Rnor_6.019887,094 - 887,243NCBIRnor6.0
Rnor_5.019885,377 - 885,526UniSTSRnor5.0
RGSC_v3.419636,451 - 636,600UniSTSRGSC3.4
Celera19674,688 - 674,837UniSTS
RH 3.4 Map190.0UniSTS
Cytogenetic Map19p14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
10 8 29 112 53 50 23 24 23 6 154 72 1 92 43 61 27 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000061648   ⟹   ENSRNOP00000058363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19678,135 - 685,390 (+)Ensembl
mRatBN7.2 Ensembl19671,719 - 678,837 (+)Ensembl
Rnor_6.0 Ensembl19880,024 - 887,144 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000128589   ⟹   ENSRNOP00000106456
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19678,142 - 685,390 (+)Ensembl
RefSeq Acc Id: NM_001013142   ⟹   NP_001013160
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819678,154 - 685,274 (+)NCBI
mRatBN7.219671,719 - 678,839 (+)NCBI
Rnor_6.019880,024 - 887,144 (+)NCBI
Rnor_5.019878,307 - 885,427 (+)NCBI
RGSC_v3.419629,381 - 636,501 (+)RGD
Celera19667,618 - 674,738 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001013160 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH78975 (Get FASTA)   NCBI Sequence Viewer  
  EDL87243 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000058363
  ENSRNOP00000058363.2
  ENSRNOP00000106456.1
RefSeq Acc Id: NP_001013160   ⟸   NM_001013142
- UniProtKB: Q6AYN6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000058363   ⟸   ENSRNOT00000061648
Ensembl Acc Id: ENSRNOP00000106456   ⟸   ENSRNOT00000128589
Protein Domains
MARVEL

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYN6-F1-model_v2 AlphaFold Q6AYN6 1-167 view protein structure

Transcriptome

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

Promoters
RGD ID:13700912
Promoter ID:EPDNEW_R11436
Type:multiple initiation site
Name:Cmtm2a_1
Description:CKLF-like MARVEL transmembrane domain containing 2A
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_6.019880,012 - 880,072EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307501 AgrOrtholog
BioCyc Gene G2FUF-6638 BioCyc
Ensembl Genes ENSRNOG00000025420 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061648 ENTREZGENE
  ENSRNOT00000061648.5 UniProtKB/TrEMBL
  ENSRNOT00000128589.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7111936 IMAGE-MGC_LOAD
InterPro Marvel UniProtKB/TrEMBL
KEGG Report rno:307616 UniProtKB/TrEMBL
MGC_CLONE MGC:93857 IMAGE-MGC_LOAD
NCBI Gene 307616 ENTREZGENE
PhenoGen Cmtm2a PhenoGen
PROSITE MARVEL UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025420 RatGTEx
UniProt A0ABK0LPF0_RAT UniProtKB/TrEMBL
  Q6AYN6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-03 Cmtm2a  CKLF-like MARVEL transmembrane domain containing 2A  Cklfsf1  chemokine-like factor super family 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Cklfsf1  chemokine-like factor super family 1  Cklfsf1_predicted  chemokine-like factor super family 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cklfsf1_predicted  chemokine-like factor super family 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED