Samsn1 (SAM domain, SH3 domain and nuclear localization signals, 1) - Rat Genome Database

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Gene: Samsn1 (SAM domain, SH3 domain and nuclear localization signals, 1) Rattus norvegicus
Analyze
Symbol: Samsn1
Name: SAM domain, SH3 domain and nuclear localization signals, 1
RGD ID: 620926
Description: Predicted to enable phosphotyrosine residue binding activity. Predicted to be involved in negative regulation of B cell activation; negative regulation of adaptive immune response; and negative regulation of peptidyl-tyrosine phosphorylation. Predicted to be located in cytosol. Predicted to be active in cytoplasm and nucleus. Orthologous to human SAMSN1 (SAM domain, SH3 domain and nuclear localization signals 1); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Nash; SAM domain, SH3 domain and nuclear localisation signals, 1; SAM domain-containing protein SAMSN-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81127,971,565 - 28,021,944 (-)NCBIGRCr8
mRatBN7.21114,484,523 - 14,534,900 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1114,483,893 - 14,534,900 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1123,110,271 - 23,160,500 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01115,836,651 - 15,886,876 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01115,004,507 - 15,054,732 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01114,252,088 - 14,405,825 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1114,253,848 - 14,304,725 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01117,910,040 - 17,960,596 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41114,633,494 - 14,683,788 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11114,633,493 - 14,683,788 (-)NCBI
Celera1114,497,563 - 14,547,805 (-)NCBICelera
Cytogenetic Map11p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
cytosol  (ISO)
nucleus  (IBA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. HACS1 encodes a novel SH3-SAM adaptor protein differentially expressed in normal and malignant hematopoietic cells. Claudio JO, etal., Oncogene 2001 Aug 30;20(38):5373-7.
2. 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.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11594764   PMID:15381729   PMID:19923443   PMID:20478393   PMID:22658674  


Genomics

Comparative Map Data
Samsn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81127,971,565 - 28,021,944 (-)NCBIGRCr8
mRatBN7.21114,484,523 - 14,534,900 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1114,483,893 - 14,534,900 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1123,110,271 - 23,160,500 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01115,836,651 - 15,886,876 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01115,004,507 - 15,054,732 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01114,252,088 - 14,405,825 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1114,253,848 - 14,304,725 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01117,910,040 - 17,960,596 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41114,633,494 - 14,683,788 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11114,633,493 - 14,683,788 (-)NCBI
Celera1114,497,563 - 14,547,805 (-)NCBICelera
Cytogenetic Map11p11NCBI
SAMSN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382114,485,228 - 14,659,417 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2114,485,228 - 14,658,821 (-)EnsemblGRCh38hg38GRCh38
GRCh372115,857,549 - 16,031,738 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362114,779,420 - 14,840,535 (-)NCBINCBI36Build 36hg18NCBI36
Build 342114,779,419 - 14,840,535NCBI
Celera211,027,395 - 1,088,492 (-)NCBICelera
Cytogenetic Map21q11.2NCBI
HuRef211,240,511 - 1,338,520 (-)NCBIHuRef
CHM1_12115,418,089 - 15,516,274 (-)NCBICHM1_1
T2T-CHM13v2.02112,840,563 - 13,014,732 (-)NCBIT2T-CHM13v2.0
Samsn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391675,655,682 - 75,706,154 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1675,655,681 - 75,819,169 (-)EnsemblGRCm39 Ensembl
GRCm381675,858,794 - 75,909,266 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1675,858,793 - 76,022,281 (-)EnsemblGRCm38mm10GRCm38
MGSCv371675,859,039 - 75,909,511 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361675,741,474 - 75,791,946 (-)NCBIMGSCv36mm8
Celera1676,082,014 - 76,131,797 (-)NCBICelera
Cytogenetic Map16C3.1NCBI
cM Map1643.36NCBI
Samsn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540716,329,288 - 16,378,062 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540716,329,838 - 16,377,763 (-)NCBIChiLan1.0ChiLan1.0
SAMSN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22210,979,161 - 11,149,950 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1215,812,917 - 5,983,746 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0211,228,632 - 1,399,331 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12114,595,688 - 14,703,600 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2114,595,688 - 14,711,613 (-)Ensemblpanpan1.1panPan2
SAMSN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13111,485,964 - 11,756,275 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3111,486,649 - 11,754,607 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3111,497,136 - 11,766,896 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03111,510,963 - 11,781,247 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3111,510,981 - 11,781,296 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13111,484,017 - 11,753,288 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03111,521,549 - 11,791,326 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03111,917,912 - 12,187,664 (-)NCBIUU_Cfam_GSD_1.0
Samsn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497112,580,579 - 12,671,795 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365057,499,719 - 7,550,679 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365057,499,801 - 7,591,566 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMSN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13179,428,779 - 179,556,447 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113179,431,494 - 179,509,359 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213189,668,581 - 189,798,767 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103218266
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1277,870,604 - 78,038,215 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl277,937,984 - 78,038,199 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605075,882,004 - 76,050,679 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Samsn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247452,977,395 - 3,022,694 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247452,977,401 - 3,022,606 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Samsn1
281 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:86
Interacting mature miRNAs:93
Transcripts:ENSRNOT00000040202
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
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
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
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111283104625121472Rat


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 2 8 19 1 10
Low 1 35 49 41 41 8 9 59 35 35 1 8
Below cutoff 8 2 15 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040202   ⟹   ENSRNOP00000039751
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1114,483,893 - 14,516,391 (-)Ensembl
Rnor_6.0 Ensembl1114,254,047 - 14,304,603 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082143   ⟹   ENSRNOP00000074870
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1114,483,893 - 14,534,900 (-)Ensembl
Rnor_6.0 Ensembl1114,253,848 - 14,304,725 (-)Ensembl
RefSeq Acc Id: NM_130821   ⟹   NP_570834
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81127,971,565 - 28,021,944 (-)NCBI
mRatBN7.21114,484,523 - 14,534,900 (-)NCBI
Rnor_6.01114,254,047 - 14,304,685 (-)NCBI
Rnor_5.01117,910,040 - 17,960,596 (-)NCBI
RGSC_v3.41114,633,494 - 14,683,788 (-)RGD
Celera1114,497,563 - 14,547,805 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_570834 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB84358 (Get FASTA)   NCBI Sequence Viewer  
  EDM10583 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000039751.3
  ENSRNOP00000074870
  ENSRNOP00000074870.1
Reference Protein Sequences
RefSeq Acc Id: NP_570834   ⟸   NM_130821
- UniProtKB: A0A0G2K960 (UniProtKB/TrEMBL),   A6JL18 (UniProtKB/TrEMBL),   G3V993 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074870   ⟸   ENSRNOT00000082143
RefSeq Acc Id: ENSRNOP00000039751   ⟸   ENSRNOT00000040202
Protein Domains
SAM   SH3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K960-F1-model_v2 AlphaFold A0A0G2K960 1-372 view protein structure

Transcriptome

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

Promoters
RGD ID:13698005
Promoter ID:EPDNEW_R8530
Type:single initiation site
Name:Samsn1_1
Description:SAM domain, SH3 domain and nuclear localization signals, 1
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_6.01114,304,696 - 14,304,756EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620926 AgrOrtholog
BioCyc Gene G2FUF-22222 BioCyc
Ensembl Genes ENSRNOG00000030930 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040202.3 UniProtKB/TrEMBL
  ENSRNOT00000082143 ENTREZGENE
  ENSRNOT00000082143.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  SH3 Domains UniProtKB/TrEMBL
InterPro rSAM/SH3_domain-containing UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM/pointed UniProtKB/TrEMBL
  SAMSN1_SAM UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
KEGG Report rno:170637 UniProtKB/TrEMBL
NCBI Gene 170637 ENTREZGENE
PANTHER SAM DOMAIN-CONTAINING PROTEIN SAMSN-1 UniProtKB/TrEMBL
  SAM-DOMAIN, SH3 AND NUCLEAR LOCALIZATION SIGNALS PROTEIN RELATED UniProtKB/TrEMBL
Pfam SAM_2 UniProtKB/TrEMBL
  SH3_2 UniProtKB/TrEMBL
  SLY UniProtKB/TrEMBL
PhenoGen Samsn1 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030930 RatGTEx
SMART SAM UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
UniProt A0A0G2K960 ENTREZGENE, UniProtKB/TrEMBL
  A6JL18 ENTREZGENE, UniProtKB/TrEMBL
  G3V993 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Samsn1  SAM domain, SH3 domain and nuclear localisation signals, 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Samsn1  SAM domain, SH3 domain and nuclear localisation signals, 1      Symbol and Name status set to provisional 70820 PROVISIONAL