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SLX9 SLX9 ribosome biogenesis factor [ Homo sapiens (human) ]

Gene ID: 85395, updated on 5-Mar-2024

Summary

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Official Symbol
SLX9provided by HGNC
Official Full Name
SLX9 ribosome biogenesis factorprovided by HGNC
Primary source
HGNC:HGNC:15811
See related
Ensembl:ENSG00000160256 AllianceGenome:HGNC:15811
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PRED56; FAM207A; C21orf70
Summary
Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleolus. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 3.9), spleen (RPKM 3.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
21q22.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44939697..44976973)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43300445..43337689)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46359612..46396888)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene integrin subunit beta 2 Neighboring gene uncharacterized LOC107987303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46329075-46329574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46333656-46334156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46337409-46338321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13395 Neighboring gene ITGB2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46345923-46346812 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:46347045-46348244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46351267-46352146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13396 Neighboring gene long intergenic non-protein coding RNA 1547 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:46359630-46360194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46369323-46369908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46369909-46370494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46371986-46372936 Neighboring gene FAM207A intron CAGE-defined mid-level expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46389870-46390685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46390686-46391500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46398896-46399794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46399795-46400691 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46406949-46407903 Neighboring gene long intergenic non-protein coding RNA 163 Neighboring gene long intergenic non-protein coding RNA 165

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Tandem affinity purification combined with inducible shRNA expression as a tool to study the maturation of macromolecular assemblies. Wyler E, et al. RNA, 2011 Jan. PMID 21097556, Free PMC Article
  2. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. Reymond A, et al. Genomics, 2001 Nov. PMID 11707072
  3. ATRX proximal protein associations boast roles beyond histone deposition. Scott WA, et al. PLoS Genet, 2021 Nov. PMID 34780483, Free PMC Article
  4. Interactome analysis reveals that lncRNA HULC promotes aerobic glycolysis through LDHA and PKM2. Wang C, et al. Nat Commun, 2020 Jun 22. PMID 32572027, Free PMC Article
  5. A protein-RNA interaction atlas of the ribosome biogenesis factor AATF. Kaiser RWJ, et al. Sci Rep, 2019 Jul 30. PMID 31363146, Free PMC Article

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FAM207A/C21orf70 is a putative trans-acting factor involved in biogenesis of the 40S ribosomal subunit.
    Title: Tandem affinity purification combined with inducible shRNA expression as a tool to study the maturation of macromolecular assemblies.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of 90S preribosome IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
part_of preribosome, small subunit precursor IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ribosome biogenesis protein SLX9 homolog
Names
family with sequence similarity 207 member A
protein FAM207A

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)

  1. NM_001316983.2 → NP_001303912.1  ribosome biogenesis protein SLX9 homolog isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
    Source sequence(s)
    BC009341, CN368049
    UniProtKB/Swiss-Prot
    Q9NSI2
    Conserved Domains (1) summary
    pfam15341
    Location:99 → 220
    SLX9; Ribosome biogenesis protein SLX9

  2. NM_001316984.2 → NP_001303913.1  ribosome biogenesis protein SLX9 homolog isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AF391114, BC009341
    Consensus CDS
    CCDS82682.1
    UniProtKB/Swiss-Prot
    Q9NSI2
    Related
    ENSP00000380926.3, ENST00000397826.8
    Conserved Domains (1) summary
    pfam15341
    Location:84 → 206
    SLX9; Ribosome biogenesis protein SLX9

  3. NM_001316985.2 → NP_001303914.1  ribosome biogenesis protein SLX9 homolog isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses two alternate in-frame splice junctions compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AL844908, AP001505, BC009341, BM042090
    UniProtKB/Swiss-Prot
    Q9NSI2
    Conserved Domains (1) summary
    pfam15341
    Location:84 → 205
    SLX9; Ribosome biogenesis protein SLX9

  4. NM_001316986.2 → NP_001303915.1  ribosome biogenesis protein SLX9 homolog isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' end compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AL844908, BC009341, BG479572, HY097926
    UniProtKB/Swiss-Prot
    Q9NSI2
    Conserved Domains (1) summary
    pfam15341
    Location:99 → 198
    SLX9; Ribosome biogenesis protein SLX9

  5. NM_001316987.2 → NP_001303916.1  ribosome biogenesis protein SLX9 homolog isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice junction in the 5' end and lacks an alternate in-frame exon in the 3' end compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AA037661, CR998572, HY097926
    Conserved Domains (1) summary
    pfam15341
    Location:84 → 183
    SLX9; Ribosome biogenesis protein SLX9

  6. NM_001316988.2 → NP_001303917.1  ribosome biogenesis protein SLX9 homolog isoform 7

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate first exon, an alternate splice junction in the 5' end, and an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (7) is shorter at the N-terminus and lacks a single internal aa compared to isoform 1.
    Source sequence(s)
    AL844908, BC009341, BG744869
    UniProtKB/Swiss-Prot
    Q9NSI2
    Conserved Domains (1) summary
    pfam15341
    Location:1 → 113
    SLX9; Ribosome biogenesis protein SLX9

  7. NM_058190.4 → NP_478070.1  ribosome biogenesis protein SLX9 homolog isoform 1

    See identical proteins and their annotated locations for NP_478070.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC009341, HY097926
    Consensus CDS
    CCDS13718.1
    UniProtKB/Swiss-Prot
    Q9NSI2
    Related
    ENSP00000291634.6, ENST00000291634.11
    Conserved Domains (1) summary
    pfam15341
    Location:99 → 221
    SLX9; Ribosome biogenesis protein SLX9

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    44939697..44976973
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028481.3 → XP_016883970.1  ribosome biogenesis protein SLX9 homolog isoform X1

    Conserved Domains (1) summary
    pfam15341
    Location:1 → 114
    SLX9; Ribosome biogenesis protein SLX9

  2. XM_017028482.3 → XP_016883971.1  ribosome biogenesis protein SLX9 homolog isoform X1

    Conserved Domains (1) summary
    pfam15341
    Location:1 → 114
    SLX9; Ribosome biogenesis protein SLX9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    43300445..43337689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324882.1 → XP_054180857.1  ribosome biogenesis protein SLX9 homolog isoform X1

  2. XM_054324883.1 → XP_054180858.1  ribosome biogenesis protein SLX9 homolog isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NSI2.2 GenPept UniProtKB/Swiss-Prot:Q9NSI2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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