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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
    mouse all
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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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