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

Gene ID: 678652, updated on 11-Apr-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. Orthologous to human KALRN (kalirin RhoGEF kinase). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
all
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Genomic context

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See kalrnb in Genome Data Viewer
Location:
chromosome: 6
Exon count:
51
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (9289802..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 serine/threonine-protein kinase pim-1-like Neighboring gene Pim proto-oncogene, serine/threonine kinase, related 70 Neighboring gene coiled-coil domain containing 14 Neighboring gene serine/threonine-protein kinase pim-1-like 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 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; kalirin
NP_001035483.1
NP_001314918.1
NP_001314919.1
XP_017212006.1

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
    Related
    ENSDARP00000133649.1, ENSDART00000161036.2

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    9289802..9455964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017356517.2 → XP_017212006.1  kalirin isoform X1

    UniProtKB/TrEMBL
    A0A8M6YZL0

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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