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DYNC2LI1 dynein cytoplasmic 2 light intermediate chain 1 [ Homo sapiens (human) ]

Gene ID: 51626, updated on 17-Jun-2019

Summary

Official Symbol
DYNC2LI1provided by HGNC
Official Full Name
dynein cytoplasmic 2 light intermediate chain 1provided by HGNC
Primary source
HGNC:HGNC:24595
See related
Ensembl:ENSG00000138036 MIM:617083
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
LIC3; D2LIC; CGI-60
Summary
This gene encodes a protein that is a component of the dynein-2 microtubule motor protein complex that plays a role in the retrograde transport of cargo in primary cilia via the intraflagellar transport system. This gene is ubiquitously expressed and its protein, which localizes to the axoneme and Golgi apparatus, interacts directly with the cytoplasmic dynein 2 heavy chain 1 protein to form part of the multi-protein dynein-2 complex. Mutations in this gene produce defects in the dynein-2 complex which result in several types of ciliopathy including short-rib thoracic dysplasia 15 with polydactyly (SRTD15). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
Expression
Ubiquitous expression in testis (RPKM 10.0), thyroid (RPKM 6.9) and 25 other tissues See more
Orthologs

Genomic context

See DYNC2LI1 in Genome Data Viewer
Location:
2p21
Exon count:
15
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (43774039..43828320)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (44001178..44055095)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene pleckstrin homology, MyTH4 and FERM domain containing H2 Neighboring gene zinc finger protein 106 homolog (mouse) pseudogene Neighboring gene uncharacterized LOC105374571 Neighboring gene RN7SK pseudogene 66 Neighboring gene ATP binding cassette subfamily G member 5 Neighboring gene uncharacterized LOC102725159 Neighboring gene ATP binding cassette subfamily G member 8 Neighboring gene RNA, U6 small nuclear 1048, pseudogene Neighboring gene leucine rich pentatricopeptide repeat containing

Genomic regions, transcripts, and products

Expression

  • 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

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
capsid gag HIV-1 CA uncoating is delayed in the presence of ciliobrevin D, a specific inhibitor of dynein-mediated motor function, indicating that dynein is involved in CA uncoating in cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cilium Assembly, organism-specific biosystem (from REACTOME)
    Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
  • Intraflagellar transport, organism-specific biosystem (from REACTOME)
    Intraflagellar transport, organism-specific biosystemIntraflagellar transport (IFT) is a motor-based process that controls the anterograde and retrograde transport of large protein complexes, ciliary cargo and structural components along the ciliary ax...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
  • Vasopressin-regulated water reabsorption, organism-specific biosystem (from KEGG)
    Vasopressin-regulated water reabsorption, organism-specific biosystemIn the kidney, the antidiuretic hormone vasopressin (AVP) is a critical regulator of water homeostasis by controlling the water movement from lumen to the interstitium for water reabsorption and adju...
  • Vasopressin-regulated water reabsorption, conserved biosystem (from KEGG)
    Vasopressin-regulated water reabsorption, conserved biosystemIn the kidney, the antidiuretic hormone vasopressin (AVP) is a critical regulator of water homeostasis by controlling the water movement from lumen to the interstitium for water reabsorption and adju...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp564A033

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to ATP-dependent microtubule motor activity, minus-end-directed IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to ATP-dependent microtubule motor activity, minus-end-directed IDA
Inferred from Direct Assay
more info
PubMed 
dynein heavy chain binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
determination of left/right symmetry IEA
Inferred from Electronic Annotation
more info
 
intraciliary retrograde transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport involved in cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport involved in cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
intraciliary transport involved in cilium assembly TAS
Traceable Author Statement
more info
 
regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
apical part of cell ISS
Inferred from Sequence or Structural Similarity
more info
 
axoneme IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axoneme ISS
Inferred from Sequence or Structural Similarity
more info
 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with ciliary basal body ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
ciliary tip TAS
Traceable Author Statement
more info
 
ciliary transition zone IDA
Inferred from Direct Assay
more info
PubMed 
cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
cilium TAS
Traceable Author Statement
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic dynein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic dynein complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic dynein complex ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
colocalizes_with cytoplasmic microtubule ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with intraciliary transport particle ISS
Inferred from Sequence or Structural Similarity
more info
 
motile cilium ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
cytoplasmic dynein 2 light intermediate chain 1

NCBI Reference Sequences (RefSeq)

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_053008.1 RefSeqGene

    Range
    5001..40972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001193464.2NP_001180393.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 4

    See identical proteins and their annotated locations for NP_001180393.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a longer protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AK223432, BC006969
    Consensus CDS
    CCDS62903.1
    UniProtKB/Swiss-Prot
    Q8TCX1
    Related
    ENSP00000474032.1, ENST00000605786.5
    Conserved Domains (1) summary
    pfam05783
    Location:2269
    DLIC; Dynein light intermediate chain (DLIC)
  2. NM_001348912.1NP_001335841.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences at its 3' end, compared to variant 1. This results in a longer protein (isoform 5) with a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC011242, AC108476
    Conserved Domains (1) summary
    pfam05783
    Location:2268
    DLIC; Dynein light intermediate chain (DLIC)
  3. NM_001348913.1NP_001335842.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice site in the middle portion of the coding region and has multiple differences at its 3' end, compared to variant 1. This results in a longer protein (isoform 6) with a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC011242, AC108476
    Conserved Domains (1) summary
    pfam05783
    Location:2269
    DLIC; Dynein light intermediate chain (DLIC)
  4. NM_015522.3NP_056337.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 2

    See identical proteins and their annotated locations for NP_056337.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK223432, BC016324, CB528979
    Consensus CDS
    CCDS46270.1
    UniProtKB/Swiss-Prot
    Q8TCX1
    Related
    ENSP00000385738.3, ENST00000406852.7
    Conserved Domains (1) summary
    pfam05783
    Location:2160
    DLIC; Dynein light intermediate chain (DLIC)
  5. NM_016008.4NP_057092.2  cytoplasmic dynein 2 light intermediate chain 1 isoform 1

    See identical proteins and their annotated locations for NP_057092.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AK223432, AY083346
    Consensus CDS
    CCDS1813.1
    UniProtKB/Swiss-Prot
    Q8TCX1
    Related
    ENSP00000260605.8, ENST00000260605.12
    Conserved Domains (2) summary
    pfam05783
    Location:2268
    DLIC; Dynein light intermediate chain (DLIC)
    cl21455
    Location:182241
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    43774039..43828320
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001012665.1: Suppressed sequence

    Description
    NM_001012665.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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