Gcsam (germinal center-associated, signaling and motility) - Rat Genome Database

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Gene: Gcsam (germinal center-associated, signaling and motility) Rattus norvegicus
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Symbol: Gcsam
Name: germinal center-associated, signaling and motility
RGD ID: 1591321
Description: Predicted to enable actin binding activity; myosin II binding activity; and protein kinase binding activity. Predicted to be involved in negative regulation of lymphocyte migration and regulation of B cell receptor signaling pathway. Orthologous to human GCSAM (germinal center associated signaling and motility); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Gcet2; germinal center expressed transcript 2; LOC685692; similar to germinal center expressed transcript 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81168,658,350 - 68,669,598 (-)NCBIGRCr8
mRatBN7.21155,195,757 - 55,207,011 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1155,196,712 - 55,206,992 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01160,168,938 - 60,180,191 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1160,170,985 - 60,180,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01164,269,535 - 64,280,811 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,688,272 - 56,696,276 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1154,719,617 - 54,730,870 (-)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17823310   PMID:23299888  


Genomics

Comparative Map Data
Gcsam
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81168,658,350 - 68,669,598 (-)NCBIGRCr8
mRatBN7.21155,195,757 - 55,207,011 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1155,196,712 - 55,206,992 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01160,168,938 - 60,180,191 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1160,170,985 - 60,180,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01164,269,535 - 64,280,811 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,688,272 - 56,696,276 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1154,719,617 - 54,730,870 (-)NCBICelera
Cytogenetic Map11q21NCBI
GCSAM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383112,120,839 - 112,133,248 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3112,120,839 - 112,133,270 (-)EnsemblGRCh38hg38GRCh38
GRCh373111,839,686 - 111,852,095 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363113,322,378 - 113,334,807 (-)NCBINCBI36Build 36hg18NCBI36
Build 343113,322,377 - 113,334,807NCBI
Celera3110,238,762 - 110,251,221 (-)NCBICelera
Cytogenetic Map3q13.2NCBI
HuRef3109,214,468 - 109,226,853 (-)NCBIHuRef
CHM1_13111,803,710 - 111,816,174 (-)NCBICHM1_1
T2T-CHM13v2.03114,841,954 - 114,854,363 (-)NCBIT2T-CHM13v2.0
Gcsam
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391645,430,803 - 45,443,230 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1645,430,743 - 45,443,230 (+)EnsemblGRCm39 Ensembl
GRCm381645,610,440 - 45,622,867 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1645,610,380 - 45,622,867 (+)EnsemblGRCm38mm10GRCm38
MGSCv371645,610,553 - 45,622,980 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361645,529,755 - 45,542,199 (+)NCBIMGSCv36mm8
Celera1645,985,716 - 45,998,346 (+)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1629.72NCBI
Gcsam
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542712,524,654 - 12,536,645 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542712,524,261 - 12,533,773 (-)NCBIChiLan1.0ChiLan1.0
GCSAM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22110,118,508 - 110,135,110 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13110,123,288 - 110,139,889 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03109,263,708 - 109,279,715 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13116,188,865 - 116,201,338 (-)NCBIpanpan1.1PanPan1.1panPan2
GCSAM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13316,742,708 - 16,754,445 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3316,744,212 - 16,754,026 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3316,846,846 - 16,858,339 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03316,989,131 - 17,000,946 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3316,990,377 - 17,000,945 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13316,792,729 - 16,804,224 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03316,838,591 - 16,850,105 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03317,389,217 - 17,400,724 (-)NCBIUU_Cfam_GSD_1.0
Gcsam
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602137,645,147 - 137,664,419 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936834922,222 - 931,253 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936834919,655 - 931,253 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GCSAM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13147,623,212 - 147,643,942 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113147,623,212 - 147,643,942 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213157,394,414 - 157,415,506 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GCSAM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12268,656,575 - 68,669,801 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2268,656,917 - 68,671,973 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604197,804,306 - 97,814,251 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gcsam
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473136,444,290 - 36,451,195 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gcsam
38 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:37
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000043020
Prediction methods: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
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111945620576331918Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 43 54 91 90 59 25 59 6 201 90 34 35 54 31

Sequence


Ensembl Acc Id: ENSRNOT00000043020   ⟹   ENSRNOP00000041206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1155,196,712 - 55,206,992 (-)Ensembl
Rnor_6.0 Ensembl1160,170,985 - 60,180,031 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000093731   ⟹   ENSRNOP00000076218
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1155,196,712 - 55,206,992 (-)Ensembl
Rnor_6.0 Ensembl1160,171,238 - 60,180,118 (-)Ensembl
RefSeq Acc Id: XM_001064866   ⟹   XP_001064866
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81168,658,350 - 68,669,586 (-)NCBI
mRatBN7.21155,195,757 - 55,207,011 (-)NCBI
Rnor_6.01160,168,938 - 60,180,191 (-)NCBI
Rnor_5.01164,269,535 - 64,280,811 (-)NCBI
RGSC_v3.41156,688,272 - 56,696,276 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248351   ⟹   XP_006248413
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81168,658,350 - 68,669,598 (-)NCBI
mRatBN7.21155,195,757 - 55,207,007 (-)NCBI
Rnor_6.01160,168,938 - 60,180,185 (-)NCBI
Rnor_5.01164,269,535 - 64,280,811 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088890   ⟹   XP_038944818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81168,658,350 - 68,669,544 (-)NCBI
mRatBN7.21155,195,757 - 55,206,969 (-)NCBI
RefSeq Acc Id: XP_001064866   ⟸   XM_001064866
- Peptide Label: isoform X1
- UniProtKB: D3ZLK1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248413   ⟸   XM_006248351
- Peptide Label: isoform X2
- UniProtKB: A0A1W2Q6E0 (UniProtKB/TrEMBL),   A6IQY4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000041206   ⟸   ENSRNOT00000043020
Ensembl Acc Id: ENSRNOP00000076218   ⟸   ENSRNOT00000093731
RefSeq Acc Id: XP_038944818   ⟸   XM_039088890
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLK1-F1-model_v2 AlphaFold D3ZLK1 1-182 view protein structure

Transcriptome

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

Promoters
RGD ID:13698136
Promoter ID:EPDNEW_R8658
Type:single initiation site
Name:Gcsam_1
Description:germinal center-associated, signaling and motility
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_6.01160,180,135 - 60,180,195EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591321 AgrOrtholog
BioCyc Gene G2FUF-21382 BioCyc
Ensembl Genes ENSRNOG00000022110 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043020.4 UniProtKB/TrEMBL
  ENSRNOT00000093731.2 UniProtKB/TrEMBL
InterPro GC_assoc_lym UniProtKB/TrEMBL
KEGG Report rno:685692 UniProtKB/TrEMBL
NCBI Gene 685692 ENTREZGENE
PANTHER GERMINAL CENTER-ASSOCIATED SIGNALING AND MOTILITY PROTEIN UniProtKB/TrEMBL
  PTHR35351 UniProtKB/TrEMBL
Pfam HGAL UniProtKB/TrEMBL
PhenoGen Gcsam PhenoGen
RatGTEx ENSRNOG00000022110 RatGTEx
UniProt A0A1W2Q6E0 ENTREZGENE, UniProtKB/TrEMBL
  A6IQY4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLK1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Gcsam  germinal center-associated, signaling and motility  LOC683566  similar to germinal center expressed transcript 2  Data merged from RGD:1585628 1643240 APPROVED
2012-10-05 Gcsam  germinal center-associated, signaling and motility  Gcet2  germinal center expressed transcript 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Gcet2  germinal center expressed transcript 2  LOC685692  similar to germinal center expressed transcript 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC685692  similar to germinal center expressed transcript 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC683566  similar to germinal center expressed transcript 2      Symbol and Name status set to provisional 70820 PROVISIONAL