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WDR47 WD repeat domain 47 [ Homo sapiens (human) ]

Gene ID: 22911, updated on 2-Nov-2024

Summary

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Official Symbol
WDR47provided by HGNC
Official Full Name
WD repeat domain 47provided by HGNC
Primary source
HGNC:HGNC:29141
See related
Ensembl:ENSG00000085433 MIM:615734; AllianceGenome:HGNC:29141
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
Summary
Predicted to act upstream of or within several processes, including detection of hot stimulus involved in thermoception; neuronal stem cell population maintenance; and telencephalon development. Predicted to be located in several cellular components, including growth cone; microtubule; and neuronal cell body. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in brain (RPKM 29.8), testis (RPKM 15.2) and 22 other tissues See more
Orthologs
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Genomic context

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See WDR47 in Genome Data Viewer
Location:
1p13.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108970214..109042102, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109003568..109075520, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109512836..109584724, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene AKNA domain containing 1 Neighboring gene spermatogenesis associated 42 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1139 Neighboring gene G protein signaling modulator 2 Neighboring gene chloride channel CLIC like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109500895-109501396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109503808-109504308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109504309-109504809 Neighboring gene Sharpr-MPRA regulatory region 7966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1140 Neighboring gene NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-like Neighboring gene ribosomal protein L17 pseudogene 7 Neighboring gene MPRA-validated peak353 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1141 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:109588748-109589027 Neighboring gene ribosomal protein S27 pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109609757-109610560 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109616882-109617868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1433 Neighboring gene RAN pseudogene 5 Neighboring gene TATA-box binding protein associated factor 13

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 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. Nemitin, a novel Map8/Map1s interacting protein with Wd40 repeats. Wang W, et al. PLoS One, 2012. PMID 22523538, Free PMC Article
  2. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery. Guardia CM, et al. Mol Biol Cell, 2021 Nov 1. PMID 34432492, Free PMC Article
  3. The centrosomal deubiquitylase USP21 regulates Gli1 transcriptional activity and stability. Heride C, et al. J Cell Sci, 2016 Nov 1. PMID 27621083, Free PMC Article
  4. High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2. Cappella M, et al. Cell Death Dis, 2018 Jun 28. PMID 29955039, Free PMC Article
  5. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 1998 Dec 31. PMID 10048485

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery.
    Title: RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery.
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

Clone Names

  • FLJ90135, KIAA0893

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 adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in anterior commissure morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in cerebral cortex radial glia-guided migration IEA
Inferred from Electronic Annotation
more info
  
involved_in corpus callosum development IEA
Inferred from Electronic Annotation
more info
  
involved_in detection of hot stimulus involved in thermoception IEA
Inferred from Electronic Annotation
more info
  
involved_in microtubule cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
involved_in motor behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of microtubule depolymerization IEA
Inferred from Electronic Annotation
more info
  
involved_in neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuronal stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in growth cone IEA
Inferred from Electronic Annotation
more info
  
located_in microtubule IEA
Inferred from Electronic Annotation
more info
  
located_in neuronal cell body IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
WD repeat-containing protein 47
Names
nemitin
neuronal enriched MAP-interacting protein

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_001142550.2 → NP_001136022.1  WD repeat-containing protein 47 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK225781, BM793705, DA221069
    Consensus CDS
    CCDS44186.1
    UniProtKB/TrEMBL
    B4DHA1
    Related
    ENSP00000383599.3, ENST00000400794.7
    Conserved Domains (4) summary
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    cd00200
    Location:614 → 923
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:619 → 667
    7WD40; WD40 repeat [structural motif]
    pfam17814
    Location:13 → 40
    LisH_TPL; LisH-like dimerisation domain

  2. NM_001142551.2 → NP_001136023.1  WD repeat-containing protein 47 isoform 3

    See identical proteins and their annotated locations for NP_001136023.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses several alternate in-frame splice sites in the 5' coding region, compared to variant 1, resulting in a protein (isoform 3) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AB020700, AK225781, BC039254, BM793705, DA221069
    Consensus CDS
    CCDS44187.1
    UniProtKB/Swiss-Prot
    A8MX09, O94967, Q5TYV7, Q5TYV8, Q5TYV9, Q8IXT7, Q8IYU9
    UniProtKB/TrEMBL
    B4DHA1
    Related
    ENSP00000358979.3, ENST00000369962.8
    Conserved Domains (5) summary
    smart00667
    Location:9 → 42
    LisH; Lissencephaly type-1-like homology motif
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    COG2319
    Location:545 → 918
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:606 → 915
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:611 → 659
    7WD40; WD40 repeat [structural motif]

  3. NM_014969.6 → NP_055784.3  WD repeat-containing protein 47 isoform 2

    See identical proteins and their annotated locations for NP_055784.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a protein (isoform 2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK225781, AK289789, BM793705
    Consensus CDS
    CCDS30787.1
    UniProtKB/TrEMBL
    B4DHA1
    Related
    ENSP00000358982.4, ENST00000369965.8
    Conserved Domains (5) summary
    smart00667
    Location:9 → 42
    LisH; Lissencephaly type-1-like homology motif
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    COG2319
    Location:546 → 919
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:607 → 916
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:612 → 660
    7WD40; WD40 repeat [structural motif]

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    108970214..109042102 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541028.4 → XP_011539330.1  WD repeat-containing protein 47 isoform X5

    See identical proteins and their annotated locations for XP_011539330.1

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (5) summary
    smart00667
    Location:9 → 42
    LisH; Lissencephaly type-1-like homology motif
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    COG2319
    Location:545 → 920
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:606 → 917
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:611 → 659
    7WD40; WD40 repeat [structural motif]

  2. XM_006710460.5 → XP_006710523.1  WD repeat-containing protein 47 isoform X4

    See identical proteins and their annotated locations for XP_006710523.1

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (5) summary
    smart00667
    Location:9 → 42
    LisH; Lissencephaly type-1-like homology motif
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    COG2319
    Location:546 → 921
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:607 → 918
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:612 → 660
    7WD40; WD40 repeat [structural motif]

  3. XM_017000696.3 → XP_016856185.1  WD repeat-containing protein 47 isoform X3

    UniProtKB/TrEMBL
    B4DHA1

  4. XM_011541027.4 → XP_011539329.1  WD repeat-containing protein 47 isoform X2

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (4) summary
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    cd00200
    Location:613 → 924
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:618 → 666
    7WD40; WD40 repeat [structural motif]
    pfam17814
    Location:13 → 40
    LisH_TPL; LisH-like dimerisation domain

  5. XM_011541029.3 → XP_011539331.1  WD repeat-containing protein 47 isoform X1

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (4) summary
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    cd00200
    Location:614 → 925
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:619 → 667
    7WD40; WD40 repeat [structural motif]
    pfam17814
    Location:13 → 40
    LisH_TPL; LisH-like dimerisation domain

  6. XM_017000697.3 → XP_016856186.1  WD repeat-containing protein 47 isoform X7

    UniProtKB/Swiss-Prot
    A8MX09, O94967, Q5TYV7, Q5TYV8, Q5TYV9, Q8IXT7, Q8IYU9
    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (5) summary
    smart00667
    Location:9 → 42
    LisH; Lissencephaly type-1-like homology motif
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    COG2319
    Location:545 → 918
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:606 → 915
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:611 → 659
    7WD40; WD40 repeat [structural motif]

  7. XM_047449522.1 → XP_047305478.1  WD repeat-containing protein 47 isoform X6

  8. XM_011541030.2 → XP_011539332.1  WD repeat-containing protein 47 isoform X4

    See identical proteins and their annotated locations for XP_011539332.1

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (5) summary
    smart00667
    Location:9 → 42
    LisH; Lissencephaly type-1-like homology motif
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    COG2319
    Location:546 → 921
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:607 → 918
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:612 → 660
    7WD40; WD40 repeat [structural motif]

  9. XM_047449501.1 → XP_047305457.1  WD repeat-containing protein 47 isoform X1

  10. XM_047449499.1 → XP_047305455.1  WD repeat-containing protein 47 isoform X1

  11. XM_024454177.2 → XP_024309945.1  WD repeat-containing protein 47 isoform X1

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (4) summary
    smart00668
    Location:45 → 102
    CTLH; C-terminal to LisH motif
    cd00200
    Location:614 → 925
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:619 → 667
    7WD40; WD40 repeat [structural motif]
    pfam17814
    Location:13 → 40
    LisH_TPL; LisH-like dimerisation domain

  12. XM_011541031.2 → XP_011539333.1  WD repeat-containing protein 47 isoform X8

    UniProtKB/TrEMBL
    B4DHA1
    Conserved Domains (2) summary
    cd00200
    Location:514 → 825
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:519 → 567
    7WD40; WD40 repeat [structural motif]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    109003568..109075520 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335210.1 → XP_054191185.1  WD repeat-containing protein 47 isoform X7

    UniProtKB/Swiss-Prot
    A8MX09, O94967, Q5TYV7, Q5TYV8, Q5TYV9, Q8IXT7, Q8IYU9

  2. XM_054335208.1 → XP_054191183.1  WD repeat-containing protein 47 isoform X5

  3. XM_054335206.1 → XP_054191181.1  WD repeat-containing protein 47 isoform X4

  4. XM_054335205.1 → XP_054191180.1  WD repeat-containing protein 47 isoform X3

  5. XM_054335204.1 → XP_054191179.1  WD repeat-containing protein 47 isoform X2

  6. XM_054335202.1 → XP_054191177.1  WD repeat-containing protein 47 isoform X1

  7. XM_054335209.1 → XP_054191184.1  WD repeat-containing protein 47 isoform X6

  8. XM_054335207.1 → XP_054191182.1  WD repeat-containing protein 47 isoform X4

  9. XM_054335203.1 → XP_054191178.1  WD repeat-containing protein 47 isoform X1

  10. XM_054335211.1 → XP_054191186.1  WD repeat-containing protein 47 isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O94967.1 GenPept UniProtKB/Swiss-Prot:O94967

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