Scamp4 (secretory carrier membrane protein 4) - Rat Genome Database

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Gene: Scamp4 (secretory carrier membrane protein 4) Rattus norvegicus
Analyze
Symbol: Scamp4
Name: secretory carrier membrane protein 4
RGD ID: 68354
Description: Predicted to be involved in exocytosis. Predicted to be located in membrane. Predicted to be active in recycling endosome membrane and trans-Golgi network membrane. Orthologous to human SCAMP4 (secretory carrier membrane protein 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: SCAMP-4; secretory carrier-associated membrane protein 4
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,752,193 - 9,764,614 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl79,752,193 - 9,778,736 (-)EnsemblGRCr8
mRatBN7.279,101,504 - 9,113,929 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,101,489 - 9,113,967 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx711,979,727 - 11,992,191 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,855,239 - 13,867,703 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,721,307 - 11,733,744 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,969,720 - 11,982,141 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,969,720 - 11,982,141 (-)Ensemblrn6Rnor6.0
Rnor_5.0712,137,245 - 12,149,666 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4710,612,354 - 10,624,775 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera77,283,714 - 7,296,113 (-)NCBICelera
RGSC_v3.1710,612,353 - 10,624,775 (-)NCBI
Cytogenetic Map7q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Expression of the SCAMP-4 gene, a new member of the secretory carrier membrane protein family, is repressed by progesterone in brain regions associated with female sexual behavior. Krebs CJ and Pfaff DW, Brain Res Mol Brain Res 2001 Mar 31;88(1-2):144-54.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Scamp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,752,193 - 9,764,614 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl79,752,193 - 9,778,736 (-)EnsemblGRCr8
mRatBN7.279,101,504 - 9,113,929 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,101,489 - 9,113,967 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx711,979,727 - 11,992,191 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,855,239 - 13,867,703 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,721,307 - 11,733,744 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,969,720 - 11,982,141 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,969,720 - 11,982,141 (-)Ensemblrn6Rnor6.0
Rnor_5.0712,137,245 - 12,149,666 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4710,612,354 - 10,624,775 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera77,283,714 - 7,296,113 (-)NCBICelera
RGSC_v3.1710,612,353 - 10,624,775 (-)NCBI
Cytogenetic Map7q11NCBI
SCAMP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38191,905,399 - 1,926,013 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl191,905,214 - 1,926,013 (+)Ensemblhg38GRCh38
GRCh37191,905,398 - 1,926,012 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36191,856,373 - 1,877,012 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34191,856,372 - 1,877,011NCBI
Celera191,839,456 - 1,860,087 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef191,676,855 - 1,697,510 (+)NCBIHuRef
CHM1_1191,904,962 - 1,925,465 (+)NCBICHM1_1
T2T-CHM13v2.0191,876,716 - 1,897,325 (+)NCBIT2T-CHM13v2.0
Scamp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,438,716 - 80,451,617 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1080,438,706 - 80,451,617 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381080,602,882 - 80,615,783 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,602,872 - 80,615,783 (+)Ensemblmm10GRCm38
MGSCv371080,065,627 - 80,078,528 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361080,006,011 - 80,018,912 (+)NCBIMGSCv36mm8
Celera1081,620,706 - 81,633,607 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
SCAMP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2206,276,368 - 6,297,165 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1195,507,395 - 5,528,107 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v019914,220 - 925,244 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1191,893,577 - 1,904,452 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl191,893,577 - 1,904,452 (+)EnsemblpanPan2panpan1.1
SCAMP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,047,022 - 57,061,274 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,048,026 - 57,063,245 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2056,840,199 - 56,868,306 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02057,778,113 - 57,806,269 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2057,778,115 - 57,848,816 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12056,835,107 - 56,863,078 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,315,013 - 57,343,088 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02057,515,962 - 57,544,107 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Scamp4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,715,026 - 216,730,688 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,104,098 - 1,119,778 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,104,098 - 1,119,761 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCAMP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,615,000 - 76,634,264 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1276,614,984 - 76,634,314 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2277,320,048 - 77,339,367 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCAMP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.161,695,545 - 1,718,633 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl61,695,876 - 1,719,189 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660817,067,161 - 7,090,361 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scamp4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11154,272,453 - 154,284,481 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Scamp4
98 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:496
Count of miRNA genes:242
Interacting mature miRNAs:293
Transcripts:ENSRNOT00000024980
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat

Markers in Region
BE095522  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,114,127 - 9,114,280 (+)MAPPERmRatBN7.2
Rnor_6.0711,982,340 - 11,982,492NCBIRnor6.0
Rnor_5.0712,149,865 - 12,150,017UniSTSRnor5.0
RGSC_v3.4710,624,974 - 10,625,126UniSTSRGSC3.4
Celera77,296,312 - 7,296,464UniSTS
RH 3.4 Map739.9UniSTS
Cytogenetic Map7q11UniSTS
BI274935  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,101,680 - 9,101,840 (+)MAPPERmRatBN7.2
Rnor_6.0711,969,897 - 11,970,056NCBIRnor6.0
Rnor_5.0712,137,422 - 12,137,581UniSTSRnor5.0
RGSC_v3.4710,612,531 - 10,612,690UniSTSRGSC3.4
Celera77,283,891 - 7,284,050UniSTS
RH 3.4 Map740.6UniSTS
Cytogenetic Map7q11UniSTS


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
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000024980   ⟹   ENSRNOP00000024980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,752,193 - 9,778,736 (-)Ensembl
mRatBN7.2 Ensembl79,101,489 - 9,113,967 (-)Ensembl
Rnor_6.0 Ensembl711,969,720 - 11,982,141 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096768   ⟹   ENSRNOP00000089473
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl79,752,193 - 9,758,292 (-)Ensembl
mRatBN7.2 Ensembl79,101,489 - 9,107,607 (-)Ensembl
RefSeq Acc Id: NM_031725   ⟹   NP_113913
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,752,193 - 9,764,614 (-)NCBI
mRatBN7.279,101,504 - 9,113,929 (-)NCBI
Rnor_6.0711,969,720 - 11,982,141 (-)NCBI
Rnor_5.0712,137,245 - 12,149,666 (-)NCBI
RGSC_v3.4710,612,354 - 10,624,775 (-)RGD
Celera77,283,714 - 7,296,113 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240999   ⟹   XP_006241061
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,752,194 - 9,764,346 (-)NCBI
mRatBN7.279,101,505 - 9,113,661 (-)NCBI
Rnor_6.0711,969,721 - 11,981,826 (-)NCBI
Rnor_5.0712,137,245 - 12,149,666 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595101   ⟹   XP_017450590
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,752,194 - 9,759,612 (-)NCBI
mRatBN7.279,101,505 - 9,108,921 (-)NCBI
Rnor_6.0711,969,721 - 11,977,560 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063264221   ⟹   XP_063120291
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,752,194 - 9,758,175 (-)NCBI
RefSeq Acc Id: NP_113913   ⟸   NM_031725
- UniProtKB: Q9ET20 (UniProtKB/Swiss-Prot),   Q5EAN5 (UniProtKB/TrEMBL),   A6K8I8 (UniProtKB/TrEMBL),   A6K8I7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241061   ⟸   XM_006240999
- Peptide Label: isoform X1
- UniProtKB: Q9ET20 (UniProtKB/Swiss-Prot),   Q5EAN5 (UniProtKB/TrEMBL),   A6K8I8 (UniProtKB/TrEMBL),   A6K8I7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450590   ⟸   XM_017595101
- Peptide Label: isoform X1
- UniProtKB: Q9ET20 (UniProtKB/Swiss-Prot),   Q5EAN5 (UniProtKB/TrEMBL),   A6K8I8 (UniProtKB/TrEMBL),   A6K8I7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000024980   ⟸   ENSRNOT00000024980
Ensembl Acc Id: ENSRNOP00000089473   ⟸   ENSRNOT00000096768
RefSeq Acc Id: XP_063120291   ⟸   XM_063264221
- Peptide Label: isoform X2
- UniProtKB: A6K8I9 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9ET20-F1-model_v2 AlphaFold Q9ET20 1-230 view protein structure

Transcriptome

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

Promoters
RGD ID:13695012
Promoter ID:EPDNEW_R5537
Type:multiple initiation site
Name:Scamp4_1
Description:secretory carrier membrane protein 4
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_6.0711,982,167 - 11,982,227EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68354 AgrOrtholog
BioCyc Gene G2FUF-34955 BioCyc
Ensembl Genes ENSRNOG00000018271 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000096768 ENTREZGENE
IMAGE_CLONE IMAGE:7304207 IMAGE-MGC_LOAD
InterPro SCAMP UniProtKB/Swiss-Prot
KEGG Report rno:65170 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105391 IMAGE-MGC_LOAD
NCBI Gene 65170 ENTREZGENE
PANTHER PTHR10687 UniProtKB/Swiss-Prot
  SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 4 UniProtKB/Swiss-Prot
Pfam SCAMP UniProtKB/Swiss-Prot
PhenoGen Scamp4 PhenoGen
RatGTEx ENSRNOG00000018271 RatGTEx
TIGR TC223708
UniProt A0A8I6GHB8_RAT UniProtKB/TrEMBL
  A0ABZ3NNB9_RAT UniProtKB/TrEMBL
  A6K8I7 ENTREZGENE, UniProtKB/TrEMBL
  A6K8I8 ENTREZGENE, UniProtKB/TrEMBL
  A6K8I9 ENTREZGENE, UniProtKB/TrEMBL
  A6K8J0_RAT UniProtKB/TrEMBL
  A6K8J1_RAT UniProtKB/TrEMBL
  Q5EAN5 ENTREZGENE
  Q9ET20 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Scamp4  secretory carrier membrane protein 4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a putative protein kinase C (PKC) phosphorylation site but lacks the putative calcium binding and leucine zipper structures, as well as protein-protein interacting NPF domains found in SCAMP family members 68304
gene_product member of family of secretory carrier membrane proteins 68304
gene_regulation expression is repressed by progesterone in the female brain 68304