Samd1 (sterile alpha motif domain containing 1) - Rat Genome Database

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Gene: Samd1 (sterile alpha motif domain containing 1) Rattus norvegicus
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Symbol: Samd1
Name: sterile alpha motif domain containing 1
RGD ID: 7529921
Description: Predicted to enable chromatin binding activity and low-density lipoprotein particle binding activity. Predicted to be involved in several processes, including lipoprotein lipid oxidation; protein homooligomerization; and regulation of gene expression. Predicted to be active in extracellular space and nucleus. Orthologous to human SAMD1 (sterile alpha motif domain containing 1); INTERACTS WITH aflatoxin B1; (-)-demecolcine (ortholog); (1->4)-beta-D-glucan (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: atherin; atherin-like; LOC102550189; LOC304649; RGD1305094; similar to CG2662-PA; sterile alpha motif domain-containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81941,055,898 - 41,059,243 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1941,055,442 - 41,059,475 (-)EnsemblGRCr8
mRatBN7.21924,151,136 - 24,154,475 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,151,128 - 24,154,488 (-)EnsemblmRatBN7.2
Rnor_6.01925,119,560 - 25,122,781 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,120,128 - 25,122,233 (+)Ensemblrn6Rnor6.0
Rnor_5.01936,096,683 - 36,099,659 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41925,837,118 - 25,839,193 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1923,699,355 - 23,701,352 (-)NCBICelera
RGSC_v3.11925,841,978 - 25,843,961 (-)NCBI
Cytogenetic Map19q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
extracellular space  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

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

Genomics

Comparative Map Data
Samd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81941,055,898 - 41,059,243 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1941,055,442 - 41,059,475 (-)EnsemblGRCr8
mRatBN7.21924,151,136 - 24,154,475 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,151,128 - 24,154,488 (-)EnsemblmRatBN7.2
Rnor_6.01925,119,560 - 25,122,781 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,120,128 - 25,122,233 (+)Ensemblrn6Rnor6.0
Rnor_5.01936,096,683 - 36,099,659 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41925,837,118 - 25,839,193 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1923,699,355 - 23,701,352 (-)NCBICelera
RGSC_v3.11925,841,978 - 25,843,961 (-)NCBI
Cytogenetic Map19q11NCBI
SAMD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381914,087,851 - 14,090,751 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1914,087,851 - 14,091,036 (-)Ensemblhg38GRCh38
GRCh371914,198,663 - 14,201,563 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361914,060,229 - 14,062,232 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341914,060,228 - 14,062,232NCBI
Celera1914,093,031 - 14,122,123 (-)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1913,770,885 - 13,799,416 (-)NCBIHuRef
CHM1_11914,199,799 - 14,201,760 (-)NCBICHM1_1
T2T-CHM13v2.01914,214,143 - 14,217,618 (-)NCBIT2T-CHM13v2.0
Samd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,724,145 - 84,727,044 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl884,724,130 - 84,727,038 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38883,997,516 - 84,000,415 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,997,501 - 84,000,409 (+)Ensemblmm10GRCm38
GRCm38.p6 Ensembl883,997,672 - 84,000,409 (+)Ensemblmm10GRCm38
MGSCv37886,521,571 - 86,524,285 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36886,887,777 - 86,890,491 (+)NCBIMGSCv36mm8
Celera888,278,279 - 88,293,704 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map840.24NCBI
Samd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541532,789,937 - 32,791,421 (-)NCBIChiLan1.0ChiLan1.0
SAMD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22019,019,983 - 19,023,265 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11918,021,672 - 18,024,901 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01913,653,166 - 13,656,397 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11914,380,192 - 14,381,843 (-)NCBIPanPan1.1PanPan1.1panPan2
SAMD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12048,427,935 - 48,430,703 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,302,467 - 48,305,418 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02048,945,742 - 48,948,700 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2048,945,757 - 48,948,390 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12048,156,927 - 48,159,873 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02048,583,486 - 48,586,439 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02048,826,306 - 48,829,256 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Samd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118207,608,258 - 207,609,749 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366592,744,967 - 2,750,135 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,096,187 - 65,099,794 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1265,096,499 - 65,099,799 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,371,876 - 65,373,944 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1612,735,255 - 12,743,871 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660746,916,107 - 6,919,352 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Samd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249011,315,854 - 1,318,152 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249011,315,309 - 1,318,167 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Samd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11716,283,847 - 16,286,573 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Samd1
12 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:40
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000007303
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)193128753251431640Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)194072709254856850Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)194072709254856850Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)194072709254856850Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)193009938347207961Rat


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000081243   ⟹   ENSRNOP00000074058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1925,120,128 - 25,122,233 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000103556   ⟹   ENSRNOP00000093467
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1941,055,442 - 41,059,475 (-)Ensembl
mRatBN7.2 Ensembl1924,151,128 - 24,154,488 (-)Ensembl
RefSeq Acc Id: XM_039098144   ⟹   XP_038954072
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81941,055,898 - 41,059,195 (-)NCBI
mRatBN7.21924,151,136 - 24,154,432 (-)NCBI
RefSeq Acc Id: XM_039098145   ⟹   XP_038954073
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81941,057,339 - 41,059,243 (-)NCBI
mRatBN7.21924,152,538 - 24,154,475 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038954072 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954073 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000093467
  ENSRNOP00000093467.1
Ensembl Acc Id: ENSRNOP00000074058   ⟸   ENSRNOT00000081243
RefSeq Acc Id: XP_038954072   ⟸   XM_039098144
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AKG2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954073   ⟸   XM_039098145
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000093467   ⟸   ENSRNOT00000103556
Protein Domains
SAM   SAMD1-like winged helix (WH)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K745-F1-model_v2 AlphaFold A0A0G2K745 1-479 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:7529921 AgrOrtholog
BioCyc Gene G2FUF-6040 BioCyc
Ensembl Genes ENSRNOG00000052637 Ensembl
  ENSRNOG00000065861 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000103556 ENTREZGENE
  ENSRNOT00000103556.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
InterPro SAM UniProtKB/TrEMBL
  SAM/pointed_sf UniProtKB/TrEMBL
  SAMD1-like_SHD UniProtKB/TrEMBL
  SAMD1-like_WH UniProtKB/TrEMBL
NCBI Gene LOC102550189 ENTREZGENE
PANTHER ATHERIN UniProtKB/TrEMBL
  UPF0575 PROTEIN C19ORF67 UniProtKB/TrEMBL
Pfam SAM_1 UniProtKB/TrEMBL
  SAMD1_SHD UniProtKB/TrEMBL
  SAMD1_WH UniProtKB/TrEMBL
PhenoGen Samd1 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
  SAMD1_WH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052637 RatGTEx
  ENSRNOG00000065861 RatGTEx
SMART SAM UniProtKB/TrEMBL
Superfamily-SCOP SSF47769 UniProtKB/TrEMBL
UniProt A0A8I6AKG2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Samd1  sterile alpha motif domain containing 1  Samd1  sterile alpha motif domain containing 1  Data merged from RGD:149736205 737654 PROVISIONAL
2021-08-09 Samd1  sterile alpha motif domain containing 1      Symbol and Name status set to provisional 45752 PROVISIONAL
2015-07-29 Samd1  sterile alpha motif domain containing 1  RGD1305094  similar to CG2662-PA  Data merged from RGD:1305094 737654 PROVISIONAL
2015-02-25 Samd1  sterile alpha motif domain containing 1  LOC102550189  atherin-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-17 LOC102550189  atherin-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1305094  similar to CG2662-PA   RGD1305094_predicted  similar to CG2662-PA (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1305094_predicted  similar to CG2662-PA (predicted)  LOC304649_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC304649_predicted  similar to CG2662-PA (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL