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    DCLK1 doublecortin like kinase 1 [ Homo sapiens (human) ]

    Gene ID: 9201, updated on 7-Apr-2024

    Summary

    Official Symbol
    DCLK1provided by HGNC
    Official Full Name
    doublecortin like kinase 1provided by HGNC
    Primary source
    HGNC:HGNC:2700
    See related
    Ensembl:ENSG00000133083 MIM:604742; AllianceGenome:HGNC:2700
    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
    CL1; DCLK; CLICK1; DCDC3A; DCAMKL1
    Summary
    This gene encodes a member of the protein kinase superfamily and the doublecortin family. The protein encoded by this gene contains two N-terminal doublecortin domains, which bind microtubules and regulate microtubule polymerization, a C-terminal serine/threonine protein kinase domain, which shows substantial homology to Ca2+/calmodulin-dependent protein kinase, and a serine/proline-rich domain in between the doublecortin and the protein kinase domains, which mediates multiple protein-protein interactions. The microtubule-polymerizing activity of the encoded protein is independent of its protein kinase activity. The encoded protein is involved in several different cellular processes, including neuronal migration, retrograde transport, neuronal apoptosis and neurogenesis. This gene is up-regulated by brain-derived neurotrophic factor and associated with memory and general cognitive abilities. Multiple transcript variants generated by two alternative promoter usage and alternative splicing have been reported, but the full-length nature and biological validity of some variants have not been defined. These variants encode different isoforms, which are differentially expressed and have different kinase activities.[provided by RefSeq, Sep 2010]
    Expression
    Biased expression in brain (RPKM 28.5), fat (RPKM 4.0) and 7 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See DCLK1 in Genome Data Viewer
    Location:
    13q13.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (35768652..36131939, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (34986929..35351445, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (36342789..36706076, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:36270618-36271214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:36271215-36271810 Neighboring gene NANOG hESC enhancer GRCh37_chr13:36286938-36287653 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:36294554-36295054 Neighboring gene long intergenic non-protein coding RNA 445 Neighboring gene NANOG hESC enhancer GRCh37_chr13:36363862-36364363 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:36429462-36430661 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:36431613-36432152 Neighboring gene uncharacterized LOC105370163 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:36432695-36433234 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:36466409-36467608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:36490885-36491627 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:36496595-36497587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7588 Neighboring gene NANOG hESC enhancer GRCh37_chr13:36567619-36568120 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:36587826-36589025 Neighboring gene nuclear-encoded mitochondrial tRNA-Gln (TTG) 10-1 Neighboring gene CCDC169-SOHLH2 readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:36728605-36729169 Neighboring gene uncharacterized LOC107984604 Neighboring gene MPRA-validated peak2068 silencer Neighboring gene spermatogenesis and oogenesis specific basic helix-loop-helix 2

    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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study of optic disc parameters.
    EBI GWAS Catalog
    Genetic variants associated with breast size also influence breast cancer risk.
    EBI GWAS Catalog
    Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association study of the age of onset of childhood asthma.
    EBI GWAS Catalog
    Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan.
    EBI GWAS Catalog
    Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0369

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein serine kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein serine/threonine kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in axon extension IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in central nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in central nervous system projection neuron axonogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endosomal transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of protein localization to nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neuron migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron projection morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein localization to nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein phosphorylation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in response to virus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    serine/threonine-protein kinase DCLK1
    Names
    doublecortin domain-containing protein 3A
    doublecortin-like and CAM kinase-like 1
    NP_001182344.1
    NP_001182345.1
    NP_001182359.1
    NP_001317000.1
    NP_001317001.1
    NP_004725.1
    XP_016876336.1
    XP_016876337.1
    XP_047286723.1
    XP_054231145.1
    XP_054231146.1
    XP_054231147.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001195415.2NP_001182344.1  serine/threonine-protein kinase DCLK1 isoform 2

      See identical proteins and their annotated locations for NP_001182344.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as DCLK-short-B, DCK-beta1 or KIAA0369-BS) is produced from the 3' promoter. It lacks several 5' exons but has an alternate 5' exon, as compared to variant 1. The resulting isoform (2) has a shorter and different N-terminus, and lacks doublecortin domains, as compared to isoform 1.
      Source sequence(s)
      AK295777, AL139083, AL157760
      Consensus CDS
      CCDS73561.1
      UniProtKB/TrEMBL
      B7Z5K4
      Related
      ENSP00000484452.1, ENST00000615680.5
      Conserved Domains (1) summary
      cd14183
      Location:76343
      STKc_DCKL1; Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1)
    2. NM_001195416.2NP_001182345.1  serine/threonine-protein kinase DCLK1 isoform 3

      See identical proteins and their annotated locations for NP_001182345.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant [3, also known as DCLK-short-A, DCK-beta2, KIAA0369-BL or cpg16 (candidate plasticity gene 16)] is produced from the 3' promoter. It lacks several 5' exons but has an alternate 5' exon, and lacks a coding exon in the 3' region that results in a frame-shift, as compared to variant 1. The resulting isoform (3) has a shorter and different N-terminus and a longer and distinct C-terminus, and lacks doublecortin domains, as compared to isoform 1.
      Source sequence(s)
      AK299059, AK311195, AL139083, AL157760, BC152456
      Consensus CDS
      CCDS55895.1
      UniProtKB/TrEMBL
      B7Z5K4
      Related
      ENSP00000369223.1, ENST00000379893.5
      Conserved Domains (1) summary
      cd14183
      Location:76343
      STKc_DCKL1; Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1)
    3. NM_001195430.2NP_001182359.1  serine/threonine-protein kinase DCLK1 isoform 4

      See identical proteins and their annotated locations for NP_001182359.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) is produced from the 3' promoter. It shares only one exon with variant 1, and encodes a 56 aa long isoform [4, also known as ania-4, or CARP (CaMK-related peptide)], which mainly consists of the serine/proline-rich domain.
      Source sequence(s)
      AL157760, BM682165
      UniProtKB/TrEMBL
      A0A9L9PXT2
      Related
      ENSP00000516676.1, ENST00000460982.1
    4. NM_001330071.2NP_001317000.1  serine/threonine-protein kinase DCLK1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate exon in the 3' coding region, resulting in a frameshift compared to variant 1. Both variants 5 and 6 encode the same isoform (5), which is longer and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK295777, AL139083, AL157760, AL160392, BC152456, BM679448, DB453639, DC350316, HY138649
      Consensus CDS
      CCDS81762.1
      UniProtKB/Swiss-Prot
      B7Z3E9, O15075, Q5VZY8, Q5VZZ0, Q5VZZ1
      UniProtKB/TrEMBL
      B7Z2T7
      Related
      ENSP00000353846.3, ENST00000360631.8
      Conserved Domains (3) summary
      cd14183
      Location:383650
      STKc_DCKL1; Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1)
      cd17069
      Location:182265
      DCX2; Dublecortin-like domain 2
      cd17140
      Location:55143
      DCX1_DCLK1; Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1)
    5. NM_001330072.2NP_001317001.1  serine/threonine-protein kinase DCLK1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, resulting in a frameshift compared to variant 1. Both variants 5 and 6 encode the same isoform (5), which is longer and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK295777, AL139083, AL157760, BC152456, BM679448, DA154341, DC350316
      Consensus CDS
      CCDS81762.1
      UniProtKB/Swiss-Prot
      B7Z3E9, O15075, Q5VZY8, Q5VZZ0, Q5VZZ1
      UniProtKB/TrEMBL
      B7Z2T7
      Conserved Domains (3) summary
      cd14183
      Location:383650
      STKc_DCKL1; Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1)
      cd17069
      Location:182265
      DCX2; Dublecortin-like domain 2
      cd17140
      Location:55143
      DCX1_DCLK1; Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1)
    6. NM_004734.5NP_004725.1  serine/threonine-protein kinase DCLK1 isoform 1

      See identical proteins and their annotated locations for NP_004725.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as DCLK-long-B, DCK-alpha1 or KIAA0369AS) is produced from the 5' promoter. It encodes the isoform 1, which includes two doublecortin domains, a serine/proline-rich domain and a protein kinase domain.
      Source sequence(s)
      AK295777, AL139083, AL157760, AL160392, BC152456
      Consensus CDS
      CCDS9354.1
      UniProtKB/TrEMBL
      B7Z2T7
      Related
      ENSP00000255448.4, ENST00000255448.8
      Conserved Domains (3) summary
      cd14183
      Location:383650
      STKc_DCKL1; Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1)
      cd17069
      Location:182265
      DCX2; Dublecortin-like domain 2
      cd17140
      Location:55143
      DCX1_DCLK1; Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      35768652..36131939 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020847.2XP_016876336.1  serine/threonine-protein kinase DCLK1 isoform X1

      UniProtKB/TrEMBL
      B7Z2T7
      Conserved Domains (3) summary
      cd14183
      Location:383650
      STKc_DCKL1; Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1)
      cd17069
      Location:182265
      DCX2; Dublecortin-like domain 2
      cd17140
      Location:55143
      DCX1_DCLK1; Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1)
    2. XM_047430767.1XP_047286723.1  serine/threonine-protein kinase DCLK1 isoform X2

      UniProtKB/TrEMBL
      Q5VZY9
    3. XM_017020848.2XP_016876337.1  serine/threonine-protein kinase DCLK1 isoform X2

      UniProtKB/TrEMBL
      Q5VZY9
      Related
      ENSP00000369222.4, ENST00000379892.4
      Conserved Domains (2) summary
      cd17069
      Location:182265
      DCX2; Dublecortin-like domain 2
      cd17140
      Location:55143
      DCX1_DCLK1; Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      34986929..35351445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375170.1XP_054231145.1  serine/threonine-protein kinase DCLK1 isoform X1

    2. XM_054375172.1XP_054231147.1  serine/threonine-protein kinase DCLK1 isoform X2

      UniProtKB/TrEMBL
      Q5VZY9
    3. XM_054375171.1XP_054231146.1  serine/threonine-protein kinase DCLK1 isoform X2

      UniProtKB/TrEMBL
      Q5VZY9