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 protein transport. Located in transport vesicle. 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,101,504 - 9,113,929 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,101,489 - 9,113,967 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,979,727 - 11,992,191 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0713,855,239 - 13,867,703 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0711,721,307 - 11,733,744 (-)NCBIRnor_WKY
Rnor_6.0711,969,720 - 11,982,141 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,969,720 - 11,982,141 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,137,245 - 12,149,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,612,354 - 10,624,775 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1710,612,353 - 10,624,775 (-)NCBI
Celera77,283,714 - 7,296,113 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
mRatBN7.279,101,504 - 9,113,929 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,101,489 - 9,113,967 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,979,727 - 11,992,191 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0713,855,239 - 13,867,703 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0711,721,307 - 11,733,744 (-)NCBIRnor_WKY
Rnor_6.0711,969,720 - 11,982,141 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,969,720 - 11,982,141 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,137,245 - 12,149,666 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,612,354 - 10,624,775 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1710,612,353 - 10,624,775 (-)NCBI
Celera77,283,714 - 7,296,113 (-)NCBICelera
Cytogenetic Map7q11NCBI
SCAMP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38191,905,399 - 1,926,013 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl191,905,214 - 1,926,013 (+)EnsemblGRCh38hg38GRCh38
GRCh37191,905,398 - 1,926,012 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36191,856,373 - 1,877,012 (+)NCBINCBI36Build 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 Ensembl
GRCm381080,602,882 - 80,615,783 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,602,872 - 80,615,783 (+)EnsemblGRCm38mm10GRCm38
MGSCv371080,065,627 - 80,078,528 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361080,006,011 - 80,018,912 (+)NCBIMGSCv36mm8
Celera1081,620,706 - 81,633,607 (+)NCBICelera
Cytogenetic Map10C1NCBI
SCAMP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1191,893,577 - 1,904,452 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl191,893,577 - 1,904,452 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v019914,220 - 925,244 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2056,840,199 - 56,868,306 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02057,778,113 - 57,806,269 (-)NCBIROS_Cfam_1.0
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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660817,067,161 - 7,090,361 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Scamp4
23 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat

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
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 3 35 44 33 13 33 2 66 30 41 11
Low 8 13 8 6 8 8 9 8 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024980   ⟹   ENSRNOP00000024980
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,101,489 - 9,113,967 (-)Ensembl
Rnor_6.0 Ensembl711,969,720 - 11,982,141 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096768   ⟹   ENSRNOP00000089473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,101,505 - 9,108,921 (-)NCBI
Rnor_6.0711,969,721 - 11,977,560 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113913   ⟸   NM_031725
- UniProtKB: Q5EAN5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241061   ⟸   XM_006240999
- Peptide Label: isoform X1
- UniProtKB: Q5EAN5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450590   ⟸   XM_017595101
- Peptide Label: isoform X1
- UniProtKB: Q5EAN5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024980   ⟸   ENSRNOT00000024980
RefSeq Acc Id: ENSRNOP00000089473   ⟸   ENSRNOT00000096768

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, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024980 ENTREZGENE
  ENSRNOP00000024980.4 UniProtKB/TrEMBL
  ENSRNOP00000089473.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024980 ENTREZGENE
  ENSRNOT00000024980.7 UniProtKB/TrEMBL
  ENSRNOT00000096768.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7304207 IMAGE-MGC_LOAD
InterPro SCAMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:65170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105391 IMAGE-MGC_LOAD
NCBI Gene 65170 ENTREZGENE
PANTHER PTHR10687 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SCAMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scamp4 PhenoGen
TIGR TC223708
UniProt A0A8I6GHB8_RAT UniProtKB/TrEMBL
  Q5EAN5 ENTREZGENE, UniProtKB/TrEMBL
  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