Alms1 ALMS1, centrosome and basal body associated protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Alms1provided by RGD
Official Full Name: ALMS1, centrosome and basal body associated proteinprovided by RGD
Primary source: RGD:1311590
See related: EnsemblRapid:ENSRNOG00000022343 AllianceGenome:RGD:1311590
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable alpha-actinin binding activity and microtubule binding activity. Involved in positive regulation of endocytosis. Located in centriole and ciliary basal body. Human ortholog(s) of this gene implicated in Alstrom syndrome. Orthologous to human ALMS1 (ALMS1 centrosome and basal body associated protein). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Testes (RPKM 226.7), Thymus (RPKM 222.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (119683085..119783471)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (118125581..118226005)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (117371544..117472310)

Chromosome 4 - NC_086022.1 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?

In this study, we show that gene deletion of ALMS1 decreases NKCC2 endocytosis establishing a link between the genetic susceptibility to hypertension, CKD, and the expression of ALMS1 through its role in a salt-reabsorbing tubular segment of the kidney. These data point to ALMS1 as a potentially novel gene involved in BP and renal function regulation.
Title: Role of Alström syndrome 1 in the regulation of blood pressure and renal function.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables alpha-actinin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endosomal transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of epithelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of planar polarity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glucose homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipid metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of epithelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ovulation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of centriole replication	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of fat cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of stress fiber assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retinal rod cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatid development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in centriole	IBA Inferred from Biological aspect of Ancestor more info
located_in centriole	IDA Inferred from Direct Assay more info	PubMed
located_in centriole	ISO Inferred from Sequence Orthology more info
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: centrosome-associated protein ALMS1

Names: Alstrom syndrome 1 homolog; Alstrom syndrome protein 1

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_001106604.2 → NP_001100074.2 centrosome-associated protein ALMS1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A8I5ZSK7

Conserved Domains (1) summary

pfam15309
Location:3120 → 3241

ALMS_motif; ALMS motif

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_086022.1 Reference GRCr8

Range

119683085..119783471

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039107348.2 → XP_038963276.1 centrosome-associated protein ALMS1 isoform X1

UniProtKB/TrEMBL

A0A8I5ZSK7

Conserved Domains (2) summary

pfam18727
Location:837 → 882

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:3522 → 3643

ALMS_motif; ALMS motif
XM_039107353.2 → XP_038963281.1 centrosome-associated protein ALMS1 isoform X7

UniProtKB/TrEMBL

F1LVG9

Conserved Domains (2) summary

pfam18727
Location:837 → 882

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:3454 → 3575

ALMS_motif; ALMS motif
XM_039107349.2 → XP_038963277.1 centrosome-associated protein ALMS1 isoform X2

UniProtKB/TrEMBL

A0A8I5ZSK7

Related

ENSRNOP00000079051.2, ENSRNOT00000101178.2

Conserved Domains (2) summary

pfam18727
Location:837 → 882

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:3519 → 3640

ALMS_motif; ALMS motif
XM_063285807.1 → XP_063141877.1 centrosome-associated protein ALMS1 isoform X8

UniProtKB/TrEMBL

F1LVG9

Related

ENSRNOP00000050674.5, ENSRNOT00000045735.7
XM_039107352.2 → XP_038963280.1 centrosome-associated protein ALMS1 isoform X5

UniProtKB/TrEMBL

A0A8I5ZSK7

Conserved Domains (2) summary

pfam18727
Location:837 → 882

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:3489 → 3610

ALMS_motif; ALMS motif
XM_039107350.2 → XP_038963278.1 centrosome-associated protein ALMS1 isoform X3

UniProtKB/TrEMBL

A0A8I5ZSK7

Related

ENSRNOP00000076984.2, ENSRNOT00000109581.2

Conserved Domains (2) summary

pfam18727
Location:825 → 870

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:3510 → 3631

ALMS_motif; ALMS motif
XM_063285805.1 → XP_063141875.1 centrosome-associated protein ALMS1 isoform X4

UniProtKB/TrEMBL

A0A8I5ZSK7
XM_063285806.1 → XP_063141876.1 centrosome-associated protein ALMS1 isoform X6

UniProtKB/TrEMBL

A0A8I5ZSK7

Related

ENSRNOP00000080223.1, ENSRNOT00000113260.2
XM_039107355.2 → XP_038963283.1 centrosome-associated protein ALMS1 isoform X10

Conserved Domains (1) summary

pfam18727
Location:837 → 882

ALMS_repeat; Alstrom syndrome repeat
XM_039107354.2 → XP_038963282.1 centrosome-associated protein ALMS1 isoform X9

UniProtKB/TrEMBL

A0A8I6G4M9

Conserved Domains (2) summary

pfam18727
Location:87 → 132

ALMS_repeat; Alstrom syndrome repeat

pfam15309
Location:2772 → 2893

ALMS_motif; ALMS motif