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DYNC2I1 dynein 2 intermediate chain 1 [ Homo sapiens (human) ]

Gene ID: 55112, updated on 2-Nov-2024

Summary

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Official Symbol
DYNC2I1provided by HGNC
Official Full Name
dynein 2 intermediate chain 1provided by HGNC
Primary source
HGNC:HGNC:21862
See related
Ensembl:ENSG00000126870 MIM:615462; AllianceGenome:HGNC:21862
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
DIC6; SRPS6; SRTD8; WDR60; FAP163; CFAP163
Summary
This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD) and may facilitate the formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes including cell cycle progression, signal transduction, apoptosis, and gene regulation. The encoded protein contains four WD repeats and may play a role in the formation of cilia. Mutations in this gene have been associated with short-rib polydactyly and Jeune syndromes. [provided by RefSeq, Mar 2014]
Expression
Broad expression in testis (RPKM 15.3), fat (RPKM 3.5) and 21 other tissues See more
Orthologs
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Genomic context

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See DYNC2I1 in Genome Data Viewer
Location:
7q36.3
Exon count:
35
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (158839245..158958698)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (160062945..160186808)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (158631936..158738880)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158526538-158527737 Neighboring gene ribosomal protein L21 pseudogene 76 Neighboring gene extended synaptotagmin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158589571-158590070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158593246-158593746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158593747-158594247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158596845-158597436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158604138-158604712 Neighboring gene Sharpr-MPRA regulatory region 8416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26933 Neighboring gene uncharacterized LOC124901796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158650125-158650666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158654251-158654750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158670703-158671380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158671381-158672057 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158702850-158704049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158735855-158736701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158749944-158750515 Neighboring gene uncharacterized LOC124901794 Neighboring gene uncharacterized LOC124901795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158768653-158769393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26936

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. Expanding the phenotype associated with biallelic WDR60 mutations: Siblings with retinal degeneration and polydactyly lacking other features of short rib thoracic dystrophies. Kakar N, et al. Am J Med Genet A, 2018 Feb. PMID 29271569
  2. Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60. McInerney-Leo AM, et al. Am J Hum Genet, 2013 Sep 5. PMID 23910462, Free PMC Article
  3. New mutations in DYNC2H1 and WDR60 genes revealed by whole-exome sequencing in two unrelated Sardinian families with Jeune asphyxiating thoracic dystrophy. Cossu C, et al. Clin Chim Acta, 2016 Apr 1. PMID 26874042
  4. Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function. Vuolo L, et al. Elife, 2018 Oct 16. PMID 30320547, Free PMC Article
  5. Structure of the dynein-2 complex and its assembly with intraflagellar transport trains. Toropova K, et al. Nat Struct Mol Biol, 2019 Sep. PMID 31451806, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. WDR60 plays a major role and TCTEX1D2 plays an auxiliary role in the dynein-2 complex to mediate retrograde ciliary protein trafficking.
    Title: Interaction of WDR60 intermediate chain with TCTEX1D2 light chain of the dynein-2 complex is crucial for ciliary protein trafficking.
  2. loss of function of dynein-2 WDR34 and WDR60 subunits leads to defects in transition zone architecture, as well as intraflagellar transport.
    Title: Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function.
  3. Our finding broadens the spectrum of WDR60-related phenotypes and shows the utility of broad multigene panels during the genetic work-up of patients with ciliopathies.
    Title: Expanding the phenotype associated with biallelic WDR60 mutations: Siblings with retinal degeneration and polydactyly lacking other features of short rib thoracic dystrophies.
  4. exome analysis allowed to identify mutations not previously reported in the DYNC2H1 (MIM 603297) and WDR60 (MIM 615462) genes, both codifying for ciliary intraflagellar transport components whose mutations are known to cause Jeune syndrome
    Title: New mutations in DYNC2H1 and WDR60 genes revealed by whole-exome sequencing in two unrelated Sardinian families with Jeune asphyxiating thoracic dystrophy.
  5. These findings show that WDR60 mutations can cause skeletal ciliopathies and suggest a role for WDR60 in ciliogenesis.
    Title: Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60.
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

Associated conditions

Description Tests
Short-rib thoracic dysplasia 8 with or without polydactyly
MedGen: C3809691 OMIM: 615503 GeneReviews: Not available
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EBI GWAS Catalog

Description
Identification of ten loci associated with height highlights new biological pathways in human growth.
EBI GWAS Catalog

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10300, FLJ23575

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables dynein heavy chain binding IEA
Inferred from Electronic Annotation
more info
  
enables dynein light chain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cilium assembly IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in embryonic skeletal system morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intraciliary retrograde transport IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
colocalizes_with centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with ciliary base IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary base IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary tip TAS
Traceable Author Statement
more info
  
located_in cilium TAS
Traceable Author Statement
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
part_of cytoplasmic dynein complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space HDA PubMed 
colocalizes_with interphase microtubule organizing center IDA
Inferred from Direct Assay
more info
 PubMed 
located_in pericentriolar material IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with spindle pole IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cytoplasmic dynein 2 intermediate chain 1
Names
WD repeat domain 60
WD repeat-containing protein 60
testicular secretory protein Li 66

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.

Genomic

  1. NG_034051.2 RefSeqGene

    Range
    22314..111945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001350914.2 → NP_001337843.1  cytoplasmic dynein 2 intermediate chain 1 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC004863, AC124833
    Conserved Domains (3) summary
    COG2319
    Location:581 → 971
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:599 → 627
    7WD40; WD40 repeat [structural motif]
    cl26511
    Location:5 → 289
    Neuromodulin_N; Gap junction protein N-terminal region

  2. NM_001350915.2 → NP_001337844.1  cytoplasmic dynein 2 intermediate chain 1 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC004863, AC124833
    Conserved Domains (2) summary
    COG2319
    Location:436 → 826
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:454 → 482
    7WD40; WD40 repeat [structural motif]

  3. NM_001350916.2 → NP_001337845.1  cytoplasmic dynein 2 intermediate chain 1 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC004863, AC124833
    UniProtKB/TrEMBL
    A4D230
    Conserved Domains (2) summary
    COG2319
    Location:140 → 530
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:426 → 462
    7WD40; WD40 repeat [structural motif]

  4. NM_001350917.2 → NP_001337846.1  cytoplasmic dynein 2 intermediate chain 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variant 6, encodes isoform e.
    Source sequence(s)
    AC004863, AC124833
    UniProtKB/TrEMBL
    A4D230
    Conserved Domains (2) summary
    COG2319
    Location:211 → 601
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:497 → 533
    7WD40; WD40 repeat [structural motif]

  5. NM_001350918.2 → NP_001337847.1  cytoplasmic dynein 2 intermediate chain 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variant 5, encodes isoform e.
    Source sequence(s)
    AC004863, AC124833
    UniProtKB/TrEMBL
    A4D230
    Conserved Domains (2) summary
    COG2319
    Location:211 → 601
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:497 → 533
    7WD40; WD40 repeat [structural motif]

  6. NM_018051.5 → NP_060521.4  cytoplasmic dynein 2 intermediate chain 1 isoform a

    See identical proteins and their annotated locations for NP_060521.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC124833, AL137660, BC014491, BM718580, DB072968
    Consensus CDS
    CCDS47757.1
    UniProtKB/Swiss-Prot
    Q8WVS4, Q9NW58
    UniProtKB/TrEMBL
    A0A140VK66
    Related
    ENSP00000384290.3, ENST00000407559.8
    Conserved Domains (3) summary
    PTZ00121
    Location:5 → 453
    PTZ00121; MAEBL; Provisional
    COG2319
    Location:627 → 1017
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:645 → 673
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    158839245..158958698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420560.1 → XP_047276516.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

  2. XM_006716041.3 → XP_006716104.1  cytoplasmic dynein 2 intermediate chain 1 isoform X3

    Conserved Domains (3) summary
    COG2319
    Location:630 → 1020
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:648 → 676
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:915 → 987
    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 ...

  3. XM_017012382.2 → XP_016867871.1  cytoplasmic dynein 2 intermediate chain 1 isoform X8

  4. XM_047420556.1 → XP_047276512.1  cytoplasmic dynein 2 intermediate chain 1 isoform X2

  5. XM_047420555.1 → XP_047276511.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

  6. XM_047420558.1 → XP_047276514.1  cytoplasmic dynein 2 intermediate chain 1 isoform X6

  7. XM_047420559.1 → XP_047276515.1  cytoplasmic dynein 2 intermediate chain 1 isoform X7

  8. XM_011516369.3 → XP_011514671.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    Conserved Domains (3) summary
    COG2319
    Location:584 → 974
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:602 → 630
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:869 → 941
    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 ...

  9. XM_011516367.3 → XP_011514669.1  cytoplasmic dynein 2 intermediate chain 1 isoform X4

    Conserved Domains (3) summary
    COG2319
    Location:630 → 1020
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:648 → 676
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:915 → 987
    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 ...

  10. XM_047420557.1 → XP_047276513.1  cytoplasmic dynein 2 intermediate chain 1 isoform X5

  11. XM_017012381.3 → XP_016867870.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    Conserved Domains (3) summary
    COG2319
    Location:584 → 974
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:602 → 630
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:869 → 941
    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 ...

  12. XM_047420561.1 → XP_047276517.1  cytoplasmic dynein 2 intermediate chain 1 isoform X9

  13. XM_047420563.1 → XP_047276519.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

  14. XM_047420562.1 → XP_047276518.1  cytoplasmic dynein 2 intermediate chain 1 isoform X11

  15. XM_017012388.2 → XP_016867877.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

    UniProtKB/TrEMBL
    A4D230
    Conserved Domains (2) summary
    COG2319
    Location:140 → 530
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:426 → 462
    7WD40; WD40 repeat [structural motif]

RNA

  1. XR_007060058.1 RNA Sequence

  2. XR_007060061.1 RNA Sequence

  3. XR_007060060.1 RNA Sequence

  4. XR_007060057.1 RNA Sequence

  5. XR_007060062.1 RNA Sequence

  6. XR_007060059.1 RNA Sequence

  7. XR_007060063.1 RNA Sequence

  8. XR_007060064.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    160062945..160186808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358564.1 → XP_054214539.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

  2. XM_054358557.1 → XP_054214532.1  cytoplasmic dynein 2 intermediate chain 1 isoform X3

  3. XM_054358565.1 → XP_054214540.1  cytoplasmic dynein 2 intermediate chain 1 isoform X8

  4. XM_054358556.1 → XP_054214531.1  cytoplasmic dynein 2 intermediate chain 1 isoform X2

  5. XM_054358555.1 → XP_054214530.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

  6. XM_054358560.1 → XP_054214535.1  cytoplasmic dynein 2 intermediate chain 1 isoform X6

  7. XM_054358561.1 → XP_054214536.1  cytoplasmic dynein 2 intermediate chain 1 isoform X7

  8. XM_054358558.1 → XP_054214533.1  cytoplasmic dynein 2 intermediate chain 1 isoform X4

  9. XM_054358559.1 → XP_054214534.1  cytoplasmic dynein 2 intermediate chain 1 isoform X5

  10. XM_054358563.1 → XP_054214538.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

  11. XM_054358562.1 → XP_054214537.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

  12. XM_054358566.1 → XP_054214541.1  cytoplasmic dynein 2 intermediate chain 1 isoform X9

  13. XM_054358567.1 → XP_054214542.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

  14. XM_054358568.1 → XP_054214543.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

RNA

  1. XR_008487646.1 RNA Sequence

  2. XR_008487648.1 RNA Sequence

  3. XR_008487647.1 RNA Sequence

  4. XR_008487645.1 RNA Sequence

  5. XR_008487650.1 RNA Sequence

  6. XR_008487649.1 RNA Sequence

  7. XR_008487651.1 RNA Sequence

  8. XR_008487652.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WVS4.3 GenPept UniProtKB/Swiss-Prot:Q8WVS4

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