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    kalrnb kalirin RhoGEF kinase b [ Danio rerio (zebrafish) ]

    Gene ID: 678652, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kalrnbprovided by ZNC
    Official Full Name
    kalirin RhoGEF kinase bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-060421-7244
    See related
    Ensembl:ENSDARG00000063538 AllianceGenome:ZFIN:ZDB-GENE-060421-7244
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fc60a10; zgc:136817
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Acts upstream of or within hemopoiesis. Predicted to be active in cytoplasm and postsynaptic density. Predicted to be extrinsic component of membrane. Is expressed in EVL. Human ortholog(s) of this gene implicated in cerebral atherosclerosis; cerebral infarction; and coronary artery disease. Orthologous to human KALRN (kalirin RhoGEF kinase). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kalrnb in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    52
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (9286491..9455964)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (9054263..9220425)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137495922 Neighboring gene coiled-coil domain containing 14 Neighboring gene serine/threonine-protein kinase pim-1 Neighboring gene cytochrome P450 family 27 subfamily A member 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Pre-gastrula expression of zebrafish extraembryonic genes. Hong SK, et al. BMC Dev Biol, 2010 Apr 27. PMID 20423468, Free PMC Article
    2. A loss of function screen of identified genome-wide association study Loci reveals new genes controlling hematopoiesis. Bielczyk-Maczyńska E, et al. PLoS Genet, 2014 Jul. PMID 25010335, Free PMC Article
    3. Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish. Kok FO, et al. Dev Cell, 2015 Jan 12. PMID 25533206, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC136817

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding 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 guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extrinsic component of membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic density IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    kalirin RhoGEF kinase b
    NP_001035483.1
    NP_001314918.1
    NP_001314919.1
    XP_068077890.1

    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.

    mRNA and Protein(s)

    1. NM_001040393.1 → NP_001035483.1  kalirin RhoGEF kinase b isoform 3

      See identical proteins and their annotated locations for NP_001035483.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      BC115278
      UniProtKB/TrEMBL
      A0A8M1N8Z4, Q1RLV0
      Related
      ENSDARP00000010346.6, ENSDART00000022620.8
      Conserved Domains (4) summary
      cd13241
      Location:225 → 358
      PH2_Kalirin_Trio_p63RhoGEF; p63RhoGEF pleckstrin homology (PH) domain, repeat 2
      pfam00169
      Location:248 → 343
      PH; PH domain
      pfam00621
      Location:51 → 221
      RhoGEF; RhoGEF domain
      cl17036
      Location:411 → 467
      SH3; Src Homology 3 domain superfamily

    2. NM_001327989.1 → NP_001314918.1  kalirin RhoGEF kinase b isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BX119909
      UniProtKB/TrEMBL
      A0A2R8RHL8, A0A8M1P9D1
      Related
      ENSDARP00000144861.1, ENSDART00000188650.1
      Conserved Domains (11) summary
      smart00150
      Location:1126 → 1214
      SPEC; Spectrin repeats
      cd11852
      Location:1641 → 1700
      SH3_Kalirin_1; First Src homology 3 domain of the RhoGEF kinase, Kalirin
      smart00516
      Location:46 → 184
      SEC14; Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p)
      cd00160
      Location:1277 → 1446
      RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
      cd00176
      Location:540 → 757
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...
      cd13240
      Location:1453 → 1575
      PH1_Kalirin_Trio_like; Triple functional domain pleckstrin homology pleckstrin homology (PH) domain, repeat 1
      cd13241
      Location:2060 → 2193
      PH2_Kalirin_Trio_p63RhoGEF; p63RhoGEF pleckstrin homology (PH) domain, repeat 2
      pfam00169
      Location:2083 → 2178
      PH; PH domain
      pfam00621
      Location:1886 → 2056
      RhoGEF; RhoGEF domain
      pfam16609
      Location:1697 → 1864
      SH3-RhoG_link; SH3-RhoGEF linking unstructured region
      cl17036
      Location:2246 → 2302
      SH3; Src Homology 3 domain superfamily

    3. NM_001327990.1 → NP_001314919.1  kalirin RhoGEF kinase b isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      BX119909
      UniProtKB/TrEMBL
      A0A0R4IJ99, A0A8M1P3E2, A0A8M6YZL0
      Related
      ENSDARP00000133649.1, ENSDART00000161036.2

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007117.7 Reference GRCz11 Primary Assembly

      Range
      9286491..9455964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068221789.1 → XP_068077890.1  kalirin RhoGEF kinase b isoform X1

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395249.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      454865..621030
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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