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

    Gene ID: 85395, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 3.9), spleen (RPKM 3.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLX9 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44939697..44976973)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43300445..43337689)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. The nucleoplasmic phase of pre-40S formation prior to nuclear export. Cheng J, et al. Nucleic Acids Res, 2022 Nov 11. PMID 36321656, Free PMC Article
    4. ATRX proximal protein associations boast roles beyond histone deposition. Scott WA, et al. PLoS Genet, 2021 Nov. PMID 34780483, Free PMC Article
    5. 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

    See all (74) 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)

    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_2024_08

    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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