Samd1 sterile alpha motif domain containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Samd1provided by MGI
Official Full Name: sterile alpha motif domain containing 1provided by MGI
Primary source: MGI:MGI:2142433
See related: Ensembl:ENSMUSG00000079003 AllianceGenome:MGI:2142433
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be located in cytoplasm and extracellular region. Predicted to be active in nucleus. Orthologous to human SAMD1 (sterile alpha motif domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 23.2), ovary adult (RPKM 17.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 8; 8 C2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (84724145..84727044)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (83997516..84000415)

Chromosome 8 - NC_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

RH124985 (e-PCR)
- UniSTS:161807

Prkaca (e-PCR), detects polymorphism
- UniSTS:144189

RH128078 (e-PCR)
- UniSTS:211386

RH94810 (e-PCR)
- UniSTS:120056

Homology

Homologs of the Samd1 gene: The Samd1 gene is conserved in human, chimpanzee, dog, and rat.
Orthologs from Annotation Pipeline: 221 organisms have orthologs with human gene Samd1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables low-density lipoprotein particle binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in foam cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in lipoprotein lipid oxidation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein homooligomerization	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sterile alpha motif domain-containing protein 1

Names: SAM domain-containing protein 1; atherin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001081415.2 → NP_001074884.1 sterile alpha motif domain-containing protein 1

See identical proteins and their annotated locations for NP_001074884.1

Status: VALIDATED

Source sequence(s)

AC156028

Consensus CDS

CCDS40404.1

UniProtKB/Swiss-Prot

D3YXK1

Related

ENSMUSP00000092853.4, ENSMUST00000095228.5

Conserved Domains (2) summary

cd09583
Location:440 → 508

SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily

smart00454
Location:440 → 506

SAM; Sterile alpha motif