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    KNDC1 kinase non-catalytic C-lobe domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 85442, updated on 14-Nov-2024

    Summary

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    Official Symbol
    KNDC1provided by HGNC
    Official Full Name
    kinase non-catalytic C-lobe domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:29374
    See related
    Ensembl:ENSG00000171798 MIM:616237; AllianceGenome:HGNC:29374
    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
    v-KIND; RASGEF2; C10orf23; Very-KIND; bB439H18.3
    Summary
    The protein encoded by this gene is a Ras guanine nucleotide exchange factor that appears to negatively regulate dendritic growth in the brain. Knockdown of this gene in senescent umbilical vein endothelial cells partially reversed the senescence, showing that this gene could potentially be targeted by anti-aging therapies. [provided by RefSeq, Dec 2016]
    Expression
    Biased expression in brain (RPKM 6.5), ovary (RPKM 2.2) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KNDC1 in Genome Data Viewer
    Location:
    10q26.3
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (133160219..133226412)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (134116905..134181903)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (134973723..135039916)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134902582-134903344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134911870-134912370 Neighboring gene adhesion G protein-coupled receptor A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134915449-134916424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134917665-134918227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134918228-134918789 Neighboring gene CEB36 minisatellite repeat instability region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134940316-134941027 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134941028-134941740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134953797-134954355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134963792-134964598 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134964599-134965404 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134965405-134966211 Neighboring gene ribosomal protein L5 pseudogene 28 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134974094-134974683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:134974684-134975274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:134979051-134979562 Neighboring gene uncharacterized LOC105378574 Neighboring gene uncharacterized LOC105378573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135013107-135013853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135013854-135014599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135038599-135039222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:135043703-135044502 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135045303-135046102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135048520-135049124 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135050334-135050937 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135050938-135051542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:135051543-135052146 Neighboring gene undifferentiated embryonic cell transcription factor 1 Neighboring gene VENT homeobox

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The results demonstrated that KNDC1 overexpression possibly inhibited HUVEC activity and function and promoted HUVEC senescence. Mechanistic studies demonstrated that KNDC1 triggered a p53ROS positive feedback loop, which serves a crucial role in regulating senescence.
      Title: Effect of KNDC1 overexpression on the senescence of human umbilical vein endothelial cells.
    2. KNDC1 knockdown promoted HUVEC proliferation via the extracellular signal-regulated kinase signaling pathway and delayed HUVEC senescence by inhibiting the p53-p21-p16 transduction cascade.
      Title: KNDC1 knockdown protects human umbilical vein endothelial cells from senescence.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ16067

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cerebellar granule cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of dendrite development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of dendrite morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of dendrite morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in small GTPase-mediated signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of guanyl-nucleotide exchange factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of guanyl-nucleotide exchange factor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    kinase non-catalytic C-lobe domain-containing protein 1
    Names
    KIND domain-containing protein 1
    RasGEF domain family, member 2
    cerebral protein 9
    kinase non-catalytic C-lobe domain (KIND) containing 1
    protein very KIND
    ras-GEF domain-containing family member 2

    NCBI Reference Sequences (RefSeq)

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    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_053178.1 RefSeqGene

      Range
      5124..71317
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001347864.2 → NP_001334793.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL445199
      Consensus CDS
      CCDS91390.1
      UniProtKB/TrEMBL
      A0A804HIZ4
      Related
      ENSP00000507288.1, ENST00000684739.1

    2. NM_001347865.2 → NP_001334794.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL445199
      Consensus CDS
      CCDS91388.1
      UniProtKB/TrEMBL
      A0A804HID6, A0A804HKF6
      Related
      ENSP00000507020.1, ENST00000682765.1

    3. NM_001347866.2 → NP_001334795.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL445199
      Consensus CDS
      CCDS91389.1
      UniProtKB/TrEMBL
      A0A804HHZ0, A0A804HKF6
      Related
      ENSP00000506821.1, ENST00000683259.1
      Conserved Domains (1) summary
      cl21453
      Location:37 → 120
      PKc_like; Protein Kinases, catalytic domain

    4. NM_152643.8 → NP_689856.6  kinase non-catalytic C-lobe domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_689856.6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL445199
      Consensus CDS
      CCDS7674.1
      UniProtKB/Swiss-Prot
      B0QZC5, Q5T233, Q6ZNH8, Q76NI1, Q8TEE5, Q96LV7, Q9C095
      Related
      ENSP00000304437.3, ENST00000304613.8
      Conserved Domains (5) summary
      cd06224
      Location:1254 → 1368
      REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
      smart00750
      Location:37 → 217
      KIND; kinase non-catalytic C-lobe domain
      pfam00617
      Location:1475 → 1673
      RasGEF; RasGEF domain
      pfam15760
      Location:215 → 333
      DLEU7; Leukemia-associated protein 7
      cl21453
      Location:444 → 608
      PKc_like; Protein Kinases, catalytic domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      133160219..133226412
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017016858.3 → XP_016872347.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      cd06224
      Location:1254 → 1368
      REM; Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately ...
      smart00750
      Location:37 → 217
      KIND; kinase non-catalytic C-lobe domain
      PHA03247
      Location:619 → 896
      PHA03247; large tegument protein UL36; Provisional
      pfam00617
      Location:1475 → 1560
      RasGEF; RasGEF domain
      cl21453
      Location:444 → 608
      PKc_like; Protein Kinases, catalytic domain

    2. XM_017016859.3 → XP_016872348.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A7I2PM36
      Related
      ENSP00000507504.1, ENST00000684081.1
      Conserved Domains (3) summary
      smart00750
      Location:37 → 217
      KIND; kinase non-catalytic C-lobe domain
      PHA03247
      Location:619 → 896
      PHA03247; large tegument protein UL36; Provisional
      cl21453
      Location:444 → 608
      PKc_like; Protein Kinases, catalytic domain

    3. XM_024448245.2 → XP_024304013.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A804HI34, A0A804HKF6
      Related
      ENSP00000506878.1, ENST00000478074.6
      Conserved Domains (1) summary
      cl21453
      Location:37 → 132
      PKc_like; Protein Kinases, catalytic domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      134116905..134181903
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367052.1 → XP_054223027.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X1

    2. XM_054367053.1 → XP_054223028.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X2

    3. XM_054367054.1 → XP_054223029.1  kinase non-catalytic C-lobe domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A804HI34
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q76NI1.2 GenPept UniProtKB/Swiss-Prot:Q76NI1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools