Scrt1 scratch family zinc finger 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scrt1provided by MGI
Official Full Name: scratch family zinc finger 1provided by MGI
Primary source: MGI:MGI:2176606
See related: Ensembl:ENSMUSG00000048385 AllianceGenome:MGI:2176606
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 DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II and regulation of neuron migration. Located in nucleus. Is expressed in future hindbrain; genitourinary system; lung epithelium; nervous system; and retina. Orthologous to human SCRT1 (scratch family transcriptional repressor 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in cerebellum adult (RPKM 40.8), cortex adult (RPKM 28.9) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 D3; 15 36.01 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (76400403..76406329, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (76516203..76522129, complement)

Chromosome 15 - NC_000081.7 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?

Scratch proteins (1 and 2) mediate the conversion of neuroepithelial cells to migrating neurons through an epithelial-mesenchymal transition.
Title: Scratch regulates neuronal migration onset via an epithelial-mesenchymal transition-like mechanism.
SCRT1 transcripts are undetectable in nearly all of the examined tumors suggesting that SCRATCH1 plays a minor role, if any, in tumorigenesis.
Title: The SNAIL family member SCRATCH1 is not expressed in human tumors.
From perinatal to adult stages, Scratch1 remains strongly expressed in almost all brain regions, although it is not found in some ventral structures such as motor nuclei and hypothalamic regions.
Title: The expression of Scratch genes in the developing and adult brain.

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General gene information

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Markers

NoName (e-PCR)
- UniSTS:494629

NoName (e-PCR)
- UniSTS:481251

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transcriptional repressor scratch 1

Names: SCRT; mScrt; scratch 1; scratch homolog 1, zinc finger protein

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_130893.3 → NP_570963.1 transcriptional repressor scratch 1

See identical proteins and their annotated locations for NP_570963.1

Status: VALIDATED

Source sequence(s)

AC157566, BC089316, CB525529

Consensus CDS

CCDS37123.1

UniProtKB/Swiss-Prot

Q99M85

Related

ENSMUSP00000094093.4, ENSMUST00000096365.5

Conserved Domains (5) summary

COG5048
Location:245 → 313

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:250 → 270

ZF_C2H2; C2H2 Zn finger [structural motif]

sd00020
Location:224 → 241

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:278 → 298

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:263 → 286

zf-H2C2_2; Zinc-finger double domain