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Aliases for DYNC2LI1 Gene

Aliases for DYNC2LI1 Gene

  • Dynein Cytoplasmic 2 Light Intermediate Chain 1 2 3 5
  • D2LIC 3 4
  • LIC3 3 4
  • Cytoplasmic Dynein 2 Light Intermediate Chain 1 3
  • Dynein 2 Light Intermediate Chain 4
  • CGI-60 3

External Ids for DYNC2LI1 Gene

Previous GeneCards Identifiers for DYNC2LI1 Gene

  • GC02P043913
  • GC02P044001

Summaries for DYNC2LI1 Gene

Entrez Gene Summary for DYNC2LI1 Gene

  • 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]

GeneCards Summary for DYNC2LI1 Gene

DYNC2LI1 (Dynein Cytoplasmic 2 Light Intermediate Chain 1) is a Protein Coding gene. Diseases associated with DYNC2LI1 include Short-Rib Thoracic Dysplasia 15 With Polydactyly and Ellis-Van Creveld Syndrome. Among its related pathways are Vasopressin-regulated water reabsorption and Organelle biogenesis and maintenance. GO annotations related to this gene include motor activity.

UniProtKB/Swiss-Prot for DYNC2LI1 Gene

  • Required for correct intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia. Involved in the regulation of ciliary length.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DYNC2LI1 Gene

Genomics for DYNC2LI1 Gene

Regulatory Elements for DYNC2LI1 Gene

Enhancers for DYNC2LI1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G043805 1.2 ENCODE dbSUPER 11.3 +33.7 33728 4.0 HNRNPUL1 FOXA2 MLX ARID4B DMAP1 YY1 ZHX2 MXD4 PPARG KAT8 ABCG5 ABCG8 DYNC2LI1 RN7SKP66 PLEKHH2 LOC105374571
GH02G043773 1.1 ENCODE 10.4 +0.2 235 1.7 PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF207 ZNF143 DEK SP3 DYNC2LI1 PLEKHH2 LOC105374571 ABCG8
GH02G043736 0.6 ENCODE 16.9 -36.6 -36558 2.2 PAF1 PKNOX1 BHLHE40 EP300 FOSL1 JUND PBX2 SCRT2 ZBTB33 FOS DYNC2LI1 PLEKHH2 RN7SKP66 LOC100421122
GH02G043818 1 Ensembl ENCODE 8 +45.3 45289 2.4 ATF1 JUN MAX FOSL1 SIRT6 ZNF548 FOS CREM L3MBTL2 NR2F1 RNU6-1048P DYNC2LI1 ABCG8 LOC105374571
GH02G043454 1.5 Ensembl ENCODE dbSUPER 5.3 -315.5 -315497 8.1 PKNOX1 FOXA2 ARID4B YY1 FOS MXD4 JUNB MIER2 PPARG TBX21 ENSG00000234936 ZFP36L2 RNU6-958P DYNC2LI1 PLEKHH2 THADA RN7SL531P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DYNC2LI1 on UCSC Golden Path with GeneCards custom track

Promoters for DYNC2LI1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000116238 361 1201 PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF207 ZNF143 DEK SP3

Genomic Location for DYNC2LI1 Gene

Chromosome:
2
Start:
43,774,039 bp from pter
End:
43,827,950 bp from pter
Size:
53,912 bases
Orientation:
Plus strand

Genomic View for DYNC2LI1 Gene

Genes around DYNC2LI1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DYNC2LI1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DYNC2LI1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DYNC2LI1 Gene

Proteins for DYNC2LI1 Gene

  • Protein details for DYNC2LI1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TCX1-DC2L1_HUMAN
    Recommended name:
    Cytoplasmic dynein 2 light intermediate chain 1
    Protein Accession:
    Q8TCX1
    Secondary Accessions:
    • A8MVJ5
    • Q53F57
    • Q6PDB2
    • Q8IWA3
    • Q96B03
    • Q96J00
    • Q9Y370
    • Q9Y3S9

    Protein attributes for DYNC2LI1 Gene

    Size:
    351 amino acids
    Molecular mass:
    39625 Da
    Quaternary structure:
    • The cytoplasmic dynein complex 2 is probably composed by a DYNC2H1 homodimer and a number of DYNC2LI1 light intermediate chains.
    SequenceCaution:
    • Sequence=AAD34055.1; Type=Frameshift; Positions=163, 167; Evidence={ECO:0000305};

    Alternative splice isoforms for DYNC2LI1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DYNC2LI1 Gene

Post-translational modifications for DYNC2LI1 Gene

  • Ubiquitination at isoforms=2329
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for DYNC2LI1 Gene

Domains & Families for DYNC2LI1 Gene

Gene Families for DYNC2LI1 Gene

Protein Domains for DYNC2LI1 Gene

Suggested Antigen Peptide Sequences for DYNC2LI1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8TCX1

UniProtKB/Swiss-Prot:

DC2L1_HUMAN :
  • Belongs to the dynein light intermediate chain family.
Family:
  • Belongs to the dynein light intermediate chain family.
genes like me logo Genes that share domains with DYNC2LI1: view

Function for DYNC2LI1 Gene

Molecular function for DYNC2LI1 Gene

UniProtKB/Swiss-Prot Function:
Required for correct intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia. Involved in the regulation of ciliary length.

Gene Ontology (GO) - Molecular Function for DYNC2LI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21252941
GO:0008569 contributes_to ATP-dependent microtubule motor activity, minus-end-directed IDA 21723285
GO:0045504 dynein heavy chain binding IBA,IEA --
genes like me logo Genes that share ontologies with DYNC2LI1: view
genes like me logo Genes that share phenotypes with DYNC2LI1: view

Human Phenotype Ontology for DYNC2LI1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DYNC2LI1 Gene

MGI Knock Outs for DYNC2LI1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for DYNC2LI1 Gene

Localization for DYNC2LI1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DYNC2LI1 Gene

Cytoplasm. Cell projection, cilium. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, cilium axoneme. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Localizes to the apical cytoplasm. {ECO:0000250 UniProtKB:Q8K0T2}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DYNC2LI1 gene
Compartment Confidence
cytoskeleton 5
cytosol 3
peroxisome 2
nucleus 2

Gene Ontology (GO) - Cellular Components for DYNC2LI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 26130459
GO:0005813 centrosome IDA 26130459
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
GO:0005868 cytoplasmic dynein complex ISS,IDA 12802074
genes like me logo Genes that share ontologies with DYNC2LI1: view

Pathways & Interactions for DYNC2LI1 Gene

genes like me logo Genes that share pathways with DYNC2LI1: view

Pathways by source for DYNC2LI1 Gene

Gene Ontology (GO) - Biological Process for DYNC2LI1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007368 determination of left/right symmetry IEA --
GO:0030030 cell projection organization IEA --
GO:0035735 intraciliary transport involved in cilium assembly TAS --
GO:0060271 cilium assembly IEA,IBA --
genes like me logo Genes that share ontologies with DYNC2LI1: view

No data available for SIGNOR curated interactions for DYNC2LI1 Gene

Drugs & Compounds for DYNC2LI1 Gene

No Compound Related Data Available

Transcripts for DYNC2LI1 Gene

Unigene Clusters for DYNC2LI1 Gene

Dynein, cytoplasmic 2, light intermediate chain 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for DYNC2LI1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15a · 15b
SP1: - - - - - -
SP2: - - - - - -
SP3: - - -
SP4: - -
SP5: -
SP6: - - -
SP7: - - - - -
SP8: -
SP9:

Relevant External Links for DYNC2LI1 Gene

GeneLoc Exon Structure for
DYNC2LI1
ECgene alternative splicing isoforms for
DYNC2LI1

Expression for DYNC2LI1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DYNC2LI1 Gene

Protein differential expression in normal tissues from HIPED for DYNC2LI1 Gene

This gene is overexpressed in Testis (48.8), Ovary (7.6), and Peripheral blood mononuclear cells (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DYNC2LI1 Gene



Protein tissue co-expression partners for DYNC2LI1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DYNC2LI1 Gene:

DYNC2LI1

SOURCE GeneReport for Unigene cluster for DYNC2LI1 Gene:

Hs.371597

mRNA Expression by UniProt/SwissProt for DYNC2LI1 Gene:

Q8TCX1-DC2L1_HUMAN
Tissue specificity: Expressed in bone, brain, kidney, and cartilage (PubMed:26077881, PubMed:26130459). Lower expression in heart, liver, lung, placenta and thymus (PubMed:26077881).

Evidence on tissue expression from TISSUES for DYNC2LI1 Gene

  • Nervous system(4.4)
  • Kidney(4.3)
genes like me logo Genes that share expression patterns with DYNC2LI1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DYNC2LI1 Gene

Orthologs for DYNC2LI1 Gene

This gene was present in the common ancestor of animals.

Orthologs for DYNC2LI1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DYNC2LI1 34 35
  • 99.24 (n)
dog
(Canis familiaris)
Mammalia DYNC2LI1 34 35
  • 92.72 (n)
cow
(Bos Taurus)
Mammalia DYNC2LI1 34 35
  • 91.36 (n)
oppossum
(Monodelphis domestica)
Mammalia DYNC2LI1 35
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dync2li1 34 16 35
  • 83.95 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia DYNC2LI1 35
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves DYNC2LI1 34 35
  • 73.1 (n)
lizard
(Anolis carolinensis)
Reptilia DYNC2LI1 35
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100498570 34
  • 70.27 (n)
zebrafish
(Danio rerio)
Actinopterygii dync2li1 34 35
  • 62.33 (n)
zgc63673 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4280 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010165 34
  • 46.27 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3769 34 35
  • 45.31 (n)
worm
(Caenorhabditis elegans)
Secernentea xbx-1 34 35
  • 50.53 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 39 (a)
OneToOne
Species where no ortholog for DYNC2LI1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DYNC2LI1 Gene

ENSEMBL:
Gene Tree for DYNC2LI1 (if available)
TreeFam:
Gene Tree for DYNC2LI1 (if available)

Paralogs for DYNC2LI1 Gene

No data available for Paralogs for DYNC2LI1 Gene

Variants for DYNC2LI1 Gene

Sequence variations from dbSNP and Humsavar for DYNC2LI1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs201948500 Pathogenic, Short-rib thoracic dysplasia 15 with polydactyly (SRTD15) [MIM:617088] 43,794,485(+) TGGAT(C/G)TTTCA reference, missense
VAR_077815 Short-rib thoracic dysplasia 15 with polydactyly (SRTD15) [MIM:617088]
rs119479065 Pathogenic 43,824,015(-) GGGTC(C/T)GAAGC intron-variant, downstream-variant-500B, reference, stop-gained
rs119479066 Pathogenic 43,826,429(-) GGAAC(C/T)GAATT intron-variant, reference, stop-gained
rs119479067 Pathogenic 43,823,981(-) GGACC(A/C/G)CGTAG intron-variant, downstream-variant-500B, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for DYNC2LI1 Gene

Variant ID Type Subtype PubMed ID
dgv59n68 CNV gain 17160897
esv3590535 CNV gain 21293372
esv3590537 CNV loss 21293372
esv3891993 CNV gain 25118596
nsv1007740 CNV gain 25217958
nsv1012126 CNV gain 25217958
nsv457174 CNV gain 19166990
nsv581661 CNV gain 21841781
nsv998912 CNV gain 25217958

Variation tolerance for DYNC2LI1 Gene

Residual Variation Intolerance Score: 77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.58; 82.55% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DYNC2LI1 Gene

Human Gene Mutation Database (HGMD)
DYNC2LI1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DYNC2LI1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DYNC2LI1 Gene

Disorders for DYNC2LI1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for DYNC2LI1 Gene - From: ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
short-rib thoracic dysplasia 15 with polydactyly
  • srtd15
ellis-van creveld syndrome
  • chondroectodermal dysplasia
asphyxiating thoracic dystrophy
  • jeune syndrome
polydactyly
  • postaxial polydactyly
short-rib thoracic dysplasia 1 with or without polydactyly
  • asphyxiating thoracic dystrophy 1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

DC2L1_HUMAN
  • Short-rib thoracic dysplasia 15 with polydactyly (SRTD15) [MIM:617088]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a trident appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269 PubMed:26077881, ECO:0000269 PubMed:26130459}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for DYNC2LI1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DYNC2LI1
genes like me logo Genes that share disorders with DYNC2LI1: view

No data available for Genatlas for DYNC2LI1 Gene

Publications for DYNC2LI1 Gene

  1. Identification of a novel light intermediate chain (D2LIC) for mammalian cytoplasmic dynein 2. (PMID: 11907264) Grissom P.M. … McIntosh J.R. (Mol. Biol. Cell 2002) 2 3 4 64
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai C.-H. … Lin W.-C. (Genome Res. 2000) 2 3 4 64
  3. Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. (PMID: 26077881) Taylor S.P. … Krakow D. (Nat Commun 2015) 3 4 64
  4. DYNC2LI1 mutations broaden the clinical spectrum of dynein-2 defects. (PMID: 26130459) Kessler K. … Thiel C.T. (Sci Rep 2015) 3 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for DYNC2LI1 Gene

Sources for DYNC2LI1 Gene

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