Synm synemin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Synmprovided by RGD
Official Full Name: syneminprovided by RGD
Primary source: RGD:727872
See related: EnsemblRapid:ENSRNOG00000014030 AllianceGenome:RGD:727872
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Dmn
Summary: Predicted to enable intermediate filament binding activity and vinculin binding activity. Predicted to be a structural constituent of cytoskeleton and structural constituent of muscle. Predicted to be involved in fast-twitch skeletal muscle fiber contraction. Located in intermediate filament. Orthologous to human SYNM (synemin). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Muscle (RPKM 843.0), Lung (RPKM 224.1) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q22

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (130743891..130774254, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (121333712..121363652, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (128692112..128722048, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Synemin promotes pulmonary artery smooth muscle cell phenotypic switch in shunt-induced pulmonary arterial hypertension.
Title: Synemin promotes pulmonary artery smooth muscle cell phenotypic switch in shunt-induced pulmonary arterial hypertension.
We conclude that beta-synemin mediates the association of desmin intermediate filaments with Z disks, whereas alpha-synemin stabilizes junctional complexes between cardiomyocytes.
Title: Synemin isoforms differentially organize cell junctions and desmin filaments in neonatal cardiomyocytes.
Retinal injury induces an upregulation of a complement of four intermediate filament proteins, including synemin and nestin, in Muller cells.
Title: Expression profiles of nestin and synemin in reactive astrocytes and Müller cells following retinal injury: a comparison with glial fibrillar acidic protein and vimentin.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH137882 (e-PCR)
- UniSTS:219969

RH143655 (e-PCR)
- UniSTS:232901

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables intermediate filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables intermediate filament binding	ISO Inferred from Sequence Orthology more info
enables structural constituent of cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of cytoskeleton	ISO Inferred from Sequence Orthology more info
enables structural constituent of muscle	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of muscle	ISO Inferred from Sequence Orthology more info
enables vinculin binding	IBA Inferred from Biological aspect of Ancestor more info
enables vinculin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in fast-twitch skeletal muscle fiber contraction	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within fast-twitch skeletal muscle fiber contraction	ISO Inferred from Sequence Orthology more info
involved_in intermediate filament cytoskeleton organization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in costamere	IBA Inferred from Biological aspect of Ancestor more info
located_in costamere	ISO Inferred from Sequence Orthology more info
is_active_in intermediate filament	IBA Inferred from Biological aspect of Ancestor more info
located_in intermediate filament	IDA Inferred from Direct Assay more info	PubMed
located_in intermediate filament	ISO Inferred from Sequence Orthology more info
located_in intermediate filament cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
is_active_in neurofilament cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in neurofilament cytoskeleton	ISO Inferred from Sequence Orthology more info
is_active_in sarcolemma	IBA Inferred from Biological aspect of Ancestor more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: synemin

Names: desmuslin; synemin, intermediate filament 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_001134858.3 → NP_001128330.1 synemin

See identical proteins and their annotated locations for NP_001128330.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A6JBT8, A6JBU1, G3V9G5

Related

ENSRNOP00000046923.3, ENSRNOT00000050832.6

Conserved Domains (3) summary

pfam00038
Location:10 → 318

Filament; Intermediate filament protein

pfam13801
Location:79 → 157

Metal_resist; Heavy-metal resistance

cl21478
Location:177 → 291

ATP-synt_B; ATP synthase B/B' CF(0)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

130743891..130774254 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006229337.4 → XP_006229399.1 synemin isoform X1

See identical proteins and their annotated locations for XP_006229399.1

UniProtKB/TrEMBL

A0A096MK54, A6JBT7, Q810D0

Related

ENSRNOP00000068384.1, ENSRNOT00000076511.4

Conserved Domains (2) summary

pfam00038
Location:10 → 318

Filament; Intermediate filament protein

pfam13801
Location:79 → 157

Metal_resist; Heavy-metal resistance

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_182737.1: Suppressed sequence

Description

NM_182737.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from chicken: DMN (GeneID:395599).