Human Gene DYNC2LI1 (ENST00000605786.5) from GENCODE V44
  Description: Homo sapiens dynein cytoplasmic 2 light intermediate chain 1 (DYNC2LI1), transcript variant 6, mRNA. (from RefSeq NM_001348913)
RefSeq Summary (NM_001193464): 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].
Gencode Transcript: ENST00000605786.5
Gencode Gene: ENSG00000138036.18
Transcript (Including UTRs)
   Position: hg38 chr2:43,774,082-43,809,997 Size: 35,916 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg38 chr2:43,774,139-43,809,767 Size: 35,629 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:43,774,082-43,809,997)mRNA (may differ from genome)Protein (352 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DC2L1_HUMAN
DESCRIPTION: RecName: Full=Cytoplasmic dynein 2 light intermediate chain 1; Short=Dynein 2 light intermediate chain;
FUNCTION: May function as a motor for intraflagellar retrograde transport. Functions in cilia biogenesis (By similarity).
SUBUNIT: The cytoplasmic dynein complex 2 is probably composed by a DYNC2H1 homodimer and a number of DYNC2LI1 light intermediate chains (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, cilium axoneme (By similarity). Cytoplasm (By similarity). Note=Localizes to the apical cytoplasm (By similarity).
SIMILARITY: Belongs to the dynein light intermediate chain family.
SEQUENCE CAUTION: Sequence=AAD34055.1; Type=Frameshift; Positions=163, 167;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DYNC2LI1
Diseases sorted by gene-association score: short-rib thoracic dysplasia 15 with polydactyly* (1242), ellis-van creveld syndrome* (217), asphyxiating thoracic dystrophy* (117), polydactyly (17), cleft lip/palate (2), visceral heterotaxy (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.45 RPKM in Testis
Total median expression: 229.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -22.6057-0.396 Picture PostScript Text
3' UTR -31.90230-0.139 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022780 - Dynein_light_int_chain

Pfam Domains:
PF05783 - Dynein light intermediate chain (DLIC)

ModBase Predicted Comparative 3D Structure on Q8TCX1
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGD  WormBase 
Protein SequenceProtein Sequence  Protein Sequence 
AlignmentAlignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003774 motor activity
GO:0005515 protein binding
GO:0045504 dynein heavy chain binding
GO:0008569 ATP-dependent microtubule motor activity, minus-end-directed

Biological Process:
GO:0007275 multicellular organism development
GO:0007368 determination of left/right symmetry
GO:0030030 cell projection organization
GO:0035721 intraciliary retrograde transport
GO:0035735 intraciliary transport involved in cilium assembly
GO:0060271 cilium assembly
GO:1902017 regulation of cilium assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005856 cytoskeleton
GO:0005868 cytoplasmic dynein complex
GO:0005874 microtubule
GO:0005929 cilium
GO:0005930 axoneme
GO:0030286 dynein complex
GO:0030990 intraciliary transport particle
GO:0031514 motile cilium
GO:0035869 ciliary transition zone
GO:0036064 ciliary basal body
GO:0042995 cell projection
GO:0045177 apical part of cell
GO:0097542 ciliary tip
GO:0005881 cytoplasmic microtubule


-  Descriptions from all associated GenBank mRNAs
  AK223432 - Homo sapiens mRNA for dynein 2 light intermediate chain isoform 1 variant, clone: FCC111B10.
BC016324 - Homo sapiens dynein, cytoplasmic 2, light intermediate chain 1, mRNA (cDNA clone MGC:23709 IMAGE:4093010), complete cds.
AK301489 - Homo sapiens cDNA FLJ60184 complete cds, highly similar to Homo sapiens dynein 2 light intermediate chain (D2LIC), transcript variant 1, mRNA.
AK074206 - Homo sapiens cDNA FLJ23626 fis, clone ADSU00926.
BC040558 - Homo sapiens dynein, cytoplasmic 2, light intermediate chain 1, mRNA (cDNA clone IMAGE:5268633), complete cds.
BC058823 - Homo sapiens dynein, cytoplasmic 2, light intermediate chain 1, mRNA (cDNA clone MGC:61923 IMAGE:4093493), complete cds.
AF151818 - Homo sapiens CGI-60 protein mRNA, complete cds.
AY083346 - Homo sapiens dynein 2 light intermediate chain (LOC51626) mRNA, complete cds.
BC006969 - Homo sapiens dynein, cytoplasmic 2, light intermediate chain 1, mRNA (cDNA clone MGC:12166 IMAGE:3828551), complete cds.
KJ906183 - Synthetic construct Homo sapiens clone ccsbBroadEn_15853 DYNC2LI1 gene, encodes complete protein.
CU691304 - Synthetic construct Homo sapiens gateway clone IMAGE:100022117 5' read DYNC2LI1 mRNA.
HQ447634 - Synthetic construct Homo sapiens clone IMAGE:100070980; CCSB013304_02 dynein, cytoplasmic 2, light intermediate chain 1 (DYNC2LI1) gene, encodes complete protein.
KJ898936 - Synthetic construct Homo sapiens clone ccsbBroadEn_08330 DYNC2LI1 gene, encodes complete protein.
KJ898937 - Synthetic construct Homo sapiens clone ccsbBroadEn_08331 DYNC2LI1 gene, encodes complete protein.
JF432876 - Synthetic construct Homo sapiens clone IMAGE:100074199 dynein, cytoplasmic 2, light intermediate chain 1 (DYNC2LI1) gene, encodes complete protein.
KJ893954 - Synthetic construct Homo sapiens clone ccsbBroadEn_03348 DYNC2LI1 gene, encodes complete protein.
AL050006 - Homo sapiens mRNA; cDNA DKFZp564A033 (from clone DKFZp564A033); partial cds.
JD184416 - Sequence 165440 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04962 - Vasopressin-regulated water reabsorption

Reactome (by CSHL, EBI, and GO)

Protein Q8TCX1 (Reactome details) participates in the following event(s):

R-HSA-5624949 Assembly of the anterograde IFT train
R-HSA-5625424 The retrograde IFT train dissociates
R-HSA-5625421 The anterograde IFT train dissociates
R-HSA-5624952 Assembly of the retrograde IFT train
R-HSA-5620924 Intraflagellar transport
R-HSA-5617833 Cilium Assembly
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: A8MVJ5, CGI-60, D2LIC, DC2L1_HUMAN, ENST00000605786.1, ENST00000605786.2, ENST00000605786.3, ENST00000605786.4, LIC3, NM_001348913, Q53F57, Q6PDB2, Q8IWA3, Q8TCX1, Q96B03, Q96J00, Q9Y370, Q9Y3S9, uc002rtl.1, uc002rtl.2, uc002rtl.3, uc002rtl.4
UCSC ID: ENST00000605786.5
RefSeq Accession: NM_001193464
Protein: Q8TCX1 (aka DC2L1_HUMAN)
CCDS: CCDS1813.1, CCDS62903.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DYNC2LI1:
evc (Ellis-van Creveld Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.