Samd1 (sterile alpha motif domain containing 1) - Rat Genome Database
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Gene: Samd1 (sterile alpha motif domain containing 1) Mus musculus
Analyze
Symbol: Samd1
Name: sterile alpha motif domain containing 1
RGD ID: 1614554
MGI Page MGI
Description: Predicted to have chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to localize to nucleus. Orthologous to human SAMD1 (sterile alpha motif domain containing 1); INTERACTS WITH 1,2-dimethylhydrazine; dibutyl phthalate; (-)-demecolcine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AA589507; atherin; SAM domain-containing protein 1; sterile alpha motif domain-containing protein 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,724,145 - 84,727,044 (+)NCBIGRCm39mm39
GRCm38883,997,516 - 84,000,415 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,997,672 - 84,000,409 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl883,997,501 - 84,000,409 (+)EnsemblGRCm38mm10GRCm38
MGSCv37886,521,571 - 86,524,285 (+)NCBIGRCm37mm9NCBIm37
MGSCv36886,887,777 - 86,890,491 (+)NCBImm8
Celera888,278,279 - 88,293,704 (+)NCBICelera
Cytogenetic Map8C2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14610273   PMID:16602821   PMID:21873635  


Genomics

Comparative Map Data
Samd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,724,145 - 84,727,044 (+)NCBIGRCm39mm39
GRCm38883,997,516 - 84,000,415 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,997,672 - 84,000,409 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl883,997,501 - 84,000,409 (+)EnsemblGRCm38mm10GRCm38
MGSCv37886,521,571 - 86,524,285 (+)NCBIGRCm37mm9NCBIm37
MGSCv36886,887,777 - 86,890,491 (+)NCBImm8
Celera888,278,279 - 88,293,704 (+)NCBICelera
Cytogenetic Map8C2NCBI
SAMD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1914,087,851 - 14,091,036 (-)EnsemblGRCh38hg38GRCh38
GRCh381914,087,851 - 14,090,751 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371914,199,229 - 14,201,232 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361914,060,229 - 14,062,232 (-)NCBINCBI36hg18NCBI36
Build 341914,060,228 - 14,062,232NCBI
Celera1914,093,031 - 14,122,123 (-)NCBI
Cytogenetic Map19p13.12NCBI
HuRef1913,770,885 - 13,799,416 (-)NCBIHuRef
CHM1_11914,199,799 - 14,201,760 (-)NCBICHM1_1
Samd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01925,119,560 - 25,122,781 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,120,128 - 25,122,233 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,096,683 - 36,099,659 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,837,118 - 25,839,193 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11925,841,978 - 25,843,961 (-)NCBI
Celera1923,699,355 - 23,701,352 (-)NCBICelera
Cytogenetic Map19q11NCBI
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
PanPan1.11914,380,192 - 14,381,843 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01913,653,166 - 13,656,397 (-)NCBIMhudiblu_PPA_v0panPan3
SAMD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12048,427,935 - 48,430,703 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Samd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366592,744,967 - 2,750,135 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1265,096,499 - 65,099,799 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,371,876 - 65,373,944 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1612,735,255 - 12,743,871 (-)NCBI
Samd1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249011,315,309 - 1,318,167 (-)NCBI

Position Markers
RH128078  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,996,060 - 83,996,278UniSTSGRCm38
MGSCv37886,519,959 - 86,520,177UniSTSGRCm37
Celera888,289,260 - 88,289,478UniSTS
Cytogenetic Map8C3UniSTS
RH94810  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38X161,484,061 - 161,484,176UniSTSGRCm38
GRCm38883,995,965 - 83,996,079UniSTSGRCm38
MGSCv37886,519,864 - 86,519,978UniSTSGRCm37
MGSCv37X157,921,993 - 157,922,108UniSTSGRCm37
Celera888,289,165 - 88,289,279UniSTS
CeleraX144,721,668 - 144,721,783UniSTS
Cytogenetic Map8C3UniSTS
RH124985  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,999,833 - 84,000,153UniSTSGRCm38
MGSCv37886,523,732 - 86,524,052UniSTSGRCm37
Celera888,293,151 - 88,293,471UniSTS
Cytogenetic Map8C3UniSTS
Prkaca  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,996,024 - 83,996,207UniSTSGRCm38
GRCm38X161,483,952 - 161,484,116UniSTSGRCm38
MGSCv37X157,921,884 - 157,922,048UniSTSGRCm37
MGSCv37886,519,923 - 86,520,106UniSTSGRCm37
Celera888,289,224 - 88,289,407UniSTS
CeleraX144,721,559 - 144,721,723UniSTS
Cytogenetic Map8C3UniSTS
cM Map8 UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
14746987Manh64_mmandible shape 64 (mouse)85005330684053306Mouse
14747005Mancz7_mmandible centroid size 7 (mouse)85005330684053306Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85188219185882191Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85428781788287993Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse
1558780Idd22_minsulin dependent diabetes susceptibility 22 (mouse)Not determined871102903105103009Mouse
4141395Char2a_mP. chabaudi malaria resistance QTL 2a (mouse)Not determined7113678390202598Mouse
4142023W3q5_mweight 3 weeks QTL 5 (mouse)Not determined71287817123895615Mouse
1357708Orq1_movulation rate QTL 1 (mouse)Not determined871287817123895615Mouse
1301872Cd4ts3_mCD4 T cell subset 3 (mouse)Not determined871396181105396393Mouse
1300920Pitm3_mprion incubation time 3 (mouse)Not determined873202495107202598Mouse
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)873400000126100000Mouse
1558890Lith18_mlithogenic gene 18 (mouse)Not determined875675517109675623Mouse
1357470Obq16_mobesity QTL 16 (mouse)Not determined875685348109685497Mouse
1301808Nhdlq1_mnon-HDL QTL 1 (mouse)Not determined875685348109685497Mouse
1301874Hdlq16_mHDL QTL 16 (mouse)Not determined875685348109685497Mouse
10412234Nhdlq14_mnon-HDL QTL 14 (mouse)Not determined875685348109685497Mouse
1301099Cbm2_mcerebellum weight 2 (mouse)Not determined878518613112518703Mouse
1301581Char2_mP. chabaudi malaria resistance QTL 2 (mouse)Not determined879082178113082403Mouse
12904012Cfq10_mconditioned fear QTL 10 (mouse)88006677589014359Mouse
10755530Wbc2_mwhite blood cell count 2 (mouse)881092664115092664Mouse
10755519Wbc1_mwhite blood cell count 1 (mouse)881619151115619151Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:253
Count of miRNA genes:186
Interacting mature miRNAs:208
Transcripts:ENSMUST00000095228
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.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001081415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC156028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000095228   ⟹   ENSMUSP00000092853
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl883,997,501 - 84,000,409 (+)Ensembl
RefSeq Acc Id: ENSMUST00000209606
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl883,998,424 - 83,998,864 (+)Ensembl
RefSeq Acc Id: NM_001081415   ⟹   NP_001074884
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39884,724,145 - 84,727,044 (+)NCBI
GRCm38883,997,516 - 84,000,415 (+)NCBI
MGSCv37886,521,571 - 86,524,285 (+)RGD
Celera888,278,279 - 88,293,704 (+)RGD
cM Map8 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_001074884 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3YXK1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001074884   ⟸   NM_001081415
- UniProtKB: D3YXK1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000092853   ⟸   ENSMUST00000095228
Protein Domains
SAM

Promoters
RGD ID:8667631
Promoter ID:EPDNEW_M11847
Type:multiple initiation site
Name:Samd1_1
Description:Mus musculus sterile alpha motif domain containing 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38883,997,638 - 83,997,698EPDNEW
RGD ID:6848892
Promoter ID:MM_TRO:9598
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3
Transcripts:MTR039498.8.1503.0
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36886,519,939 - 86,520,439 (+)MPROMDB
RGD ID:6843691
Promoter ID:MM_KWN:55039
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_001081415
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36886,520,611 - 86,522,432 (+)MPROMDB
RGD ID:6848894
Promoter ID:MM_TRO:9599
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day2,   3T3L1_Day3,   Kidney,   MEF_B6
Transcripts:MTR039498.8.1503.2
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36886,522,424 - 86,522,924 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2142433 AgrOrtholog
Ensembl Genes ENSMUSG00000079003 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000092853 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000095228 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot
InterPro SAM UniProtKB/Swiss-Prot
  SAM/pointed_sf UniProtKB/Swiss-Prot
KEGG Report mmu:666704 UniProtKB/Swiss-Prot
MGD MGI:2142433 ENTREZGENE
NCBI Gene 666704 ENTREZGENE
Pfam SAM_1 UniProtKB/Swiss-Prot
PhenoGen Samd1 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/Swiss-Prot
SMART SAM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot
UniProt D3YXK1 ENTREZGENE, UniProtKB/Swiss-Prot