SLX1B SLX1 homolog B, structure-specific endonuclease subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLX1Bprovided by HGNC
Official Full Name: SLX1 homolog B, structure-specific endonuclease subunitprovided by HGNC
Primary source: HGNC:HGNC:28748
See related: Ensembl:ENSG00000181625 MIM:615823; AllianceGenome:HGNC:28748
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GIYD2
Summary: This gene encodes a protein that is an important regulator of genome stability. The protein represents the catalytic subunit of the SLX1-SLX4 structure-specific endonuclease, which can resolve DNA secondary structures that are formed during repair and recombination processes. Two identical copies of this gene are located on the p arm of chromosome 16 due to a segmental duplication; this record represents the more telomeric copy. Alternative splicing results in multiple transcript variants. Read-through transcription also occurs between this gene and the downstream SULT1A4 (sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4) gene. [provided by RefSeq, Nov 2010]
Expression: Ubiquitous expression in duodenum (RPKM 33.7), small intestine (RPKM 28.9) and 24 other tissues See more
Orthologs: all
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Genomic context

Location:: 16p11.2

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (29454533..29458220)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (29736324..29740011)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (29465854..29469541)

Chromosome 16 - NC_000016.10 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH103211 (e-PCR)
- UniSTS:97544

RH133600 (e-PCR)
- UniSTS:216883

Readthrough SLX1B-SULT1A4

Readthrough gene: SLX1B-SULT1A4, Included gene: SULT1A4

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 5'-flap endonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5'-flap endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables crossover junction DNA endonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables crossover junction DNA endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA double-strand break processing involved in repair via single-strand annealing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair via homologous recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of telomere maintenance via telomere lengthening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of t-circle formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in t-circle formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in t-circle formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in telomere maintenance via telomere lengthening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomeric D-loop disassembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Slx1-Slx4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Slx1-Slx4 complex	IDA Inferred from Direct Assay more info	PubMed
part_of Slx1-Slx4 complex	TAS Traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: structure-specific endonuclease subunit SLX1

Names: GIY-YIG domain-containing protein 1; SLX1 structure-specific endonuclease subunit homolog B

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_001400286.1 → NP_001387215.1 structure-specific endonuclease subunit SLX1 isoform 3

Status: REVIEWED

Source sequence(s)

AC133555

UniProtKB/TrEMBL

Q9H5H2
NM_001400287.1 → NP_001387216.1 structure-specific endonuclease subunit SLX1 isoform 4

Status: REVIEWED

Source sequence(s)

AC133555
NM_024044.5 → NP_076949.1 structure-specific endonuclease subunit SLX1 isoform 1

See identical proteins and their annotated locations for NP_076949.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC133555

Consensus CDS

CCDS10648.1

UniProtKB/Swiss-Prot

B7ZME1, Q6NTG6, Q9BQ83

UniProtKB/TrEMBL

Q9H5H2

Related

ENSP00000328940.5, ENST00000330181.10

Conserved Domains (1) summary

cd10455
Location:13 → 89

GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs
NM_178044.4 → NP_835145.1 structure-specific endonuclease subunit SLX1 isoform 2

See identical proteins and their annotated locations for NP_835145.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.

Source sequence(s)

AC133555

Consensus CDS

CCDS10649.1

UniProtKB/Swiss-Prot

Q9BQ83

Related

ENSP00000335316.4, ENST00000351581.4

Conserved Domains (1) summary

cd10455
Location:13 → 82

GIY-YIG_SLX1; Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs