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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 Intraflagellar transport 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.

Additional gene information for DYNC2LI1 Gene

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
GH02H043209 1.9 FANTOM5 Ensembl ENCODE dbSUPER 12.2 -563.1 -563067 1 HDGF PKNOX1 FOXA2 MLX ARID4B DMAP1 ZNF766 MCM3 SP5 ZHX2 RNU6-1048P PLEKHH2 THADA VDAC1P13 PDSS1P2 OXER1 DYNC2LI1 ZFP36L2 C1GALT1C1L LOC100506047
GH02H043104 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.9 -666.1 -666057 6 HDGF PKNOX1 FOXA2 ARNT RAD21 RARA ZNF23 EGR1 RUNX3 CREM DYNC2LI1 OXER1 THADA GC02M043092 LOC105374570 RNU6-242P
GH02H043048 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.9 -723.2 -723161 4 SIN3A RAD21 RARA RFX5 ZNF23 RCOR1 FOS ATF7 DEK SMARCC1 RNU6-1048P PLEKHH2 THADA DYNC2LI1 ENSG00000233978 PIR48377
GH02H043805 1.2 ENCODE dbSUPER 11.3 +33.7 33728 4 FOXA2 MLX ARID4B DMAP1 YY1 ATF7 ZHX2 MXD4 REST PPARG ABCG5 ABCG8 DYNC2LI1 RN7SKP66 PLEKHH2 LOC105374571
GH02H043773 1.1 ENCODE 10.4 +0.2 235 1 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF207 ZNF143 DEK SP3 ZHX2 THADA DYNC2LI1 PLEKHH2 LOC105374571 ABCG8
- 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 ZFP64 ARID4B SIN3A DMAP1 ZNF207 ZNF143 DEK SP3 ZHX2

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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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.

Phenotypes From GWAS Catalog for DYNC2LI1 Gene

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 IEA,IBA --
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

Clone Products

  • Applied Biological Materials Clones for DYNC2LI1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

Subcellular locations from the

Human Protein Atlas (HPA)

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 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:0035721 intraciliary retrograde transport IBA --
GO:0035735 intraciliary transport involved in cilium assembly TAS,IMP --
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

Clone Products

  • Applied Biological Materials Clones for DYNC2LI1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 33 34
  • 99.24 (n)
dog
(Canis familiaris)
Mammalia DYNC2LI1 33 34
  • 92.72 (n)
cow
(Bos Taurus)
Mammalia DYNC2LI1 33 34
  • 91.36 (n)
oppossum
(Monodelphis domestica)
Mammalia DYNC2LI1 34
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Dync2li1 33 16 34
  • 83.95 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia DYNC2LI1 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves DYNC2LI1 33 34
  • 73.1 (n)
lizard
(Anolis carolinensis)
Reptilia DYNC2LI1 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100498570 33
  • 70.27 (n)
zebrafish
(Danio rerio)
Actinopterygii dync2li1 33 34
  • 62.33 (n)
zgc63673 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4280 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010165 33
  • 46.27 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3769 34 33
  • 45.31 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea xbx-1 33 34
  • 50.53 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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: HGMD, OMIM, 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
cleft lip/palate
  • alveolar cleft lip and palate
- 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 PM … McIntosh JR (Molecular biology of the cell 2002) 2 3 4 60
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4 60
  3. DYNC2LI1 mutations broaden the clinical spectrum of dynein-2 defects. (PMID: 26130459) Kessler K … Thiel CT (Scientific reports 2015) 3 4 60
  4. Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. (PMID: 26077881) Taylor SP … Krakow D (Nature communications 2015) 3 4 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for DYNC2LI1 Gene

Sources for DYNC2LI1 Gene

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