smc5 structural maintenance of chromosomes 5 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: smc5provided by ZNC
Official Full Name: structural maintenance of chromosomes 5provided by ZNC
Primary source: ZFIN:ZDB-GENE-061013-288
See related: Ensembl:ENSDARG00000044282 AllianceGenome:ZFIN:ZDB-GENE-061013-288
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: pufa; pum3; SMC5L1; zgc:66377; wu:fb70d10; wu:fi47h05; zgc:152845
Summary: Predicted to enable single-stranded DNA binding activity. Acts upstream of or within cartilage morphogenesis and regulation of apoptotic process involved in development. Predicted to be located in chromosome, telomeric region. Predicted to be part of Smc5-Smc6 complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in mosaic variegated aneuploidy syndrome. Orthologous to human SMC5 (structural maintenance of chromosomes 5). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 10

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (15618098..15644940, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (15659979..15686821, complement)

Chromosome 10 - NC_007121.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Knockdown of puf-A in zebrafish embryos resulted in microphthalmia, a small head, and abnormal primordial germ-cell (PGC) migration
Title: A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA recombination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cartilage morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within double-strand break repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair via homologous recombination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of apoptotic process involved in development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Smc5-Smc6 complex	IEA Inferred from Electronic Annotation more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: structural maintenance of chromosomes protein 5

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_001193541.1 → NP_001180470.1 structural maintenance of chromosomes protein 5

Status: VALIDATED

Source sequence(s)

BX640501

UniProtKB/Swiss-Prot

A0A8M1NV01, E7F0W1

Related

ENSDARP00000111416.3, ENSDART00000122170.4

Conserved Domains (2) summary

cd03277
Location:950 → 1052

ABC_SMC5_euk; ATP-binding cassette domain of eukaryotic SMC5 proteins

COG1196
Location:42 → 1030

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007121.7 Reference GRCz11 Primary Assembly

Range

15618098..15644940 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001077572.1: Suppressed sequence

Description

NM_001077572.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: SMC5 (GeneID:23137).
NM_201210.1: Suppressed sequence

Description

NM_201210.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.