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

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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 located in membrane. Orthologous to human CMTM2 (CKLF like MARVEL transmembrane domain containing 2).
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 Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819678,154 - 685,274 (+)NCBIGRCr8
mRatBN7.219671,719 - 678,839 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19671,719 - 678,837 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx19667,469 - 674,643 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,434,271 - 1,441,445 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019709,482 - 716,657 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.019880,024 - 887,144 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19880,024 - 887,144 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019878,307 - 885,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419629,381 - 636,501 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.119629,380 - 636,501 (+)NCBI
Celera19667,618 - 674,738 (+)NCBICelera
Cytogenetic Map19p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (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
12 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat

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
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 7
Medium 1 1
Low 1 2 5 2 5 2 4 6 16 17 3 4 4
Below cutoff 2 22 24 13 12 13 2 2 51 15 24 6 2

Sequence


RefSeq Acc Id: ENSRNOT00000061648   ⟹   ENSRNOP00000058363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19671,719 - 678,837 (+)Ensembl
Rnor_6.0 Ensembl19880,024 - 887,144 (+)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
RefSeq Acc Id: NP_001013160   ⟸   NM_001013142
- UniProtKB: Q6AYN6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000058363   ⟸   ENSRNOT00000061648
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
  ENSRNOT00000061648.4 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 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