Sectm1a (secreted and transmembrane 1A) - Rat Genome Database

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Gene: Sectm1a (secreted and transmembrane 1A) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Sectm1a
Name: secreted and transmembrane 1A
RGD ID: 1305973
Description: Predicted to enable cytokine activity. Predicted to be involved in immune response and signal transduction. Predicted to be active in membrane. Orthologous to human SECTM1 (secreted and transmembrane 1).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287885; secreted and transmembrane 1; Sectm1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210106,337,623 - 106,348,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10106,337,624 - 106,348,601 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10111,441,312 - 111,452,326 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.010110,904,372 - 110,915,388 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.010106,258,074 - 106,269,056 (-)NCBIRnor_WKY
Rnor_6.010110,263,782 - 110,274,797 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10110,263,783 - 110,274,768 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010109,850,607 - 109,861,612 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410110,283,747 - 110,294,733 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110110,298,251 - 110,309,237 (-)NCBI
Celera10104,876,384 - 104,887,372 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IBA)

Molecular Function

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 GOA human gene data--August 2006 GOA 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.

Genomics

Variants

.
Variants in Sectm1a
100 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:328
Count of miRNA genes:195
Interacting mature miRNAs:230
Transcripts:ENSRNOT00000054931
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat


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 4 4 11 4 7
Low 3 3 47 31 8 31 1 1 21 23 25 7 1
Below cutoff 31 6 6 6 7 8 25 6 5 4 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000054931   ⟹   ENSRNOP00000051814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,337,624 - 106,348,601 (-)Ensembl
Rnor_6.0 Ensembl10110,263,783 - 110,274,768 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101568   ⟹   ENSRNOP00000081653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,339,051 - 106,348,601 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106292   ⟹   ENSRNOP00000090881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,337,627 - 106,348,601 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115371   ⟹   ENSRNOP00000092336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,337,624 - 106,341,391 (-)Ensembl
RefSeq Acc Id: NM_001013043   ⟹   NP_001013061
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,337,623 - 106,348,601 (-)NCBI
Rnor_6.010110,263,782 - 110,274,768 (-)NCBI
Rnor_5.010109,850,607 - 109,861,612 (-)NCBI
RGSC_v3.410110,283,747 - 110,294,733 (-)RGD
Celera10104,876,384 - 104,887,372 (-)RGD
Sequence:
RefSeq Acc Id: XM_006247885   ⟹   XP_006247947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,337,627 - 106,348,656 (-)NCBI
Rnor_6.010110,263,786 - 110,274,797 (-)NCBI
Rnor_5.010109,850,607 - 109,861,612 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039085694   ⟹   XP_038941622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,338,353 - 106,348,656 (-)NCBI
RefSeq Acc Id: XR_005489767
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210106,338,370 - 106,348,656 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001013061 (Get FASTA)   NCBI Sequence Viewer  
  XP_006247947 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941622 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH78937 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001013061   ⟸   NM_001013043
- Peptide Label: precursor
- UniProtKB: Q6AYS0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006247947   ⟸   XM_006247885
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000051814   ⟸   ENSRNOT00000054931
RefSeq Acc Id: XP_038941622   ⟸   XM_039085694
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000090881   ⟸   ENSRNOT00000106292
RefSeq Acc Id: ENSRNOP00000092336   ⟸   ENSRNOT00000115371
RefSeq Acc Id: ENSRNOP00000081653   ⟸   ENSRNOT00000101568

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYS0-F1-model_v2 AlphaFold Q6AYS0 1-201 view protein structure

Transcriptome

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

Promoters
RGD ID:13697987
Promoter ID:EPDNEW_R8511
Type:multiple initiation site
Name:Sectm1a_1
Description:secreted and transmembrane 1A
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_6.010110,274,761 - 110,274,821EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305973 AgrOrtholog
BioCyc Gene G2FUF-22372 BioCyc
Ensembl Genes ENSRNOG00000036672 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051814 ENTREZGENE
  ENSRNOP00000051814.2 UniProtKB/TrEMBL
  ENSRNOP00000081653.1 UniProtKB/TrEMBL
  ENSRNOP00000090881 ENTREZGENE
  ENSRNOP00000090881.1 UniProtKB/TrEMBL
  ENSRNOP00000092336.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000054931 ENTREZGENE
  ENSRNOT00000054931.3 UniProtKB/TrEMBL
  ENSRNOT00000101568.1 UniProtKB/TrEMBL
  ENSRNOT00000106292 ENTREZGENE
  ENSRNOT00000106292.1 UniProtKB/TrEMBL
  ENSRNOT00000115371.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7108345 IMAGE-MGC_LOAD
InterPro Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  SECTM1 UniProtKB/TrEMBL
KEGG Report rno:287885 UniProtKB/TrEMBL
MGC_CLONE MGC:93752 IMAGE-MGC_LOAD
NCBI Gene 287885 ENTREZGENE
PANTHER PTHR15123 UniProtKB/TrEMBL
PhenoGen Sectm1a PhenoGen
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A8I5ZTC8_RAT UniProtKB/TrEMBL
  A0A8I6AEM6_RAT UniProtKB/TrEMBL
  A0A8I6AHD3_RAT UniProtKB/TrEMBL
  Q6AYS0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-25 Sectm1a  secreted and transmembrane 1A  Sectm1  secreted and transmembrane 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-02-02 Sectm1  secreted and transmembrane 1  Sectm1a  secreted and transmembrane 1A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-09-25 Sectm1a  secreted and transmembrane 1A  Sectm1_predicted  secreted and transmembrane 1 (predicted)  Symbol and name updated to reflect mouse gene nomenclature 1299863 APPROVED
2005-01-12 Sectm1_predicted  secreted and transmembrane 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED