Kalrn Gene Detail

Summary

• Symbol
  Kalrn
• Name
  kalirin, RhoGEF kinase
• Synonyms
  2210407G14Rik, E530005C20Rik, Hapip, LOC224126

• Feature Type
  protein coding gene
• IDs
  MGI:2685385
  NCBI Gene: 545156
• Alliance
  genome feature page
• Transcription Start Sites
  35 TSS

Location &
Maps

• Sequence Map
  Chr16:33789443-34393647 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 16, 24.27 cM
• Mapping Data
  3 experiments

Strain
Comparison

• SNPs within 2kb
  16565 from dbSNP Build 142
• Strain Annotations
  24

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2685385	protein coding gene	Chr16:33789443-34393902 (-)
129S1/SvImJ	ENSMUSGG00200054405	protein coding gene	Chr16:30991900-31103120 (-)
A/J	ENSMUSGG00195055203	protein coding gene	Chr16:30537881-30959980 (-)
A/J	ENSMUSG00195010724	protein coding gene	Chr16:30355652-30483670 (-)
AKR/J	ENSMUSG00220027070	protein coding gene	Chr16:30641550-30769600 (-)
AKR/J	ENSMUSGG00220054684	protein coding gene	Chr16:30824543-30935691 (-)
BALB/cJ	ENSMUSGG00180055374	protein coding gene	Chr16:30753773-31175859 (-)
BALB/cJ	ENSMUSG00180012972	protein coding gene	Chr16:30571510-30699568 (-)
C3H/HeJ	ENSMUSGG00175055068	protein coding gene	Chr16:30889195-31000393 (-)
C3H/HeJ	ENSMUSG00175028986	protein coding gene	Chr16:30713619-30834195 (-)
C57BL/6NJ	ENSMUSG00215012366	protein coding gene	Chr16:30596471-30724524 (-)
C57BL/6NJ	ENSMUSGG00215055569	protein coding gene	Chr16:30779465-30890651 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020695	protein coding gene	Chr16:31007810-31609905 (-)
CAST/EiJ	no annotation
CBA/J	ENSMUSGG00210054521	protein coding gene	Chr16:30930683-31378522 (-)
CBA/J	ENSMUSG00210027695	protein coding gene	Chr16:30755513-30876087 (-)
DBA/2J	ENSMUSGG00185057353	protein coding gene	Chr16:30845900-31278878 (-)
DBA/2J	ENSMUSG00185023619	protein coding gene	Chr16:30671063-30791633 (-)
FVB/NJ	ENSMUSGG00205054342	protein coding gene	Chr16:30869292-31291083 (-)
FVB/NJ	ENSMUSG00205018087	protein coding gene	Chr16:30686726-30814798 (-)
JF1/MsJ	no annotation
LP/J	ENSMUSGG00230055567	protein coding gene	Chr16:33421981-33844140 (-)
NOD/ShiLtJ	ENSMUSG00190020264	protein coding gene	Chr16:30863564-30991596 (-)
NOD/ShiLtJ	ENSMUSGG00190054625	protein coding gene	Chr16:31045805-31468065 (-)
NZO/HlLtJ	ENSMUSGG00225055423	protein coding gene	Chr16:36664761-37086783 (-)
NZO/HlLtJ	ENSMUSG00225038033	protein coding gene	Chr16:36482512-36610551 (-)
PWK/PhJ	no annotation
SPRET/EiJ	no annotation
WSB/EiJ	no annotation

Homology

• Human Ortholog
  KALRN, kalirin RhoGEF kinase

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  KALRN, kalirin RhoGEF kinase
  
• Synonyms
  ARHGEF24, CHDS5, DUET, DUO, HAPIP, KALNC2, TRAD
• Links
  HGNC:4814

  NCBI Gene ID: 8997

  UniProt: O60229

  
  
• Chr Location
  3q21.1-q21.2; chr3:124033369-124726325 (+)  GRCh38

---

• MGI Vertebrate Homology
  Kalrn stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: KALRN
• Gene Tree
  Kalrn
  

Human Diseases

• Diseases
  3 with human KALRN associations

				Human Disease	Mouse Models
				cerebral atherosclerosis IDs cerebral atherosclerosis       DOID:12720 ICD10CM:I67.2 ICD9CM:437.0 MESH:D002537 NCI:C34459 UMLS_CUI:C0007775
				cerebral infarction IDs cerebral infarction       DOID:3526 ICD10CM:I63 MESH:D002544 NCI:C50486 OMIM:601367 UMLS_CUI:C0007785
				coronary artery disease IDs coronary artery disease       DOID:3393 DOID:10506 DOID:3363 DOID:3394 DOID:9420 EFO:0001645 ICD10CM:I20-I25 ICD10CM:I25 ICD10CM:I25.10 ICD9CM:410-414.99 ICD9CM:414.0 ICD9CM:414.9 MESH:D003324 MESH:D003327 MESH:D017202 NCI:C35505 NCI:C50625 OMIM:300464 OMIM:607339 OMIM:608316 OMIM:608318 OMIM:608320 OMIM:610947 OMIM:611139 OMIM:612030 OMIM:614293 UMLS_CUI:C0010054 UMLS_CUI:C0010068 UMLS_CUI:C0151744 UMLS_CUI:C0264694

Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  44 phenotypes from 4 alleles in 6 genetic backgrounds
  3 images
  29 phenotype references
  

• All Mutations and Alleles
  20
• Endonuclease-mediated
  2
• Gene trapped
  13
• Targeted
  5
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  171 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a knock-out allele specific for isoform 7 exhibit decreased anxiety-related behavior, contextual conditioning, and synapse formation. Mice homozygous for another knock-out allele exhibit impaired AMPA-mediated synaptic currents and abnormal behavior.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  42
• GO References
  11

Expression

• Assay Results
  601
• Tissues
  4
• cDNA Data
  22
• Literature Summary
  4

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  GEISHA KALRN
  Xenbase kalrn

Sequences &
Gene Models

• All Sequences
  198
• RefSeq
  99
• UniProt
  9
• CCDS
  CCDS49836.1

• Ensembl
  ENSMUSG00000061751 (Evidence)
• NCBI Gene
  545156

Representative Sequences			Length	Strain/Species
genomic	545156	NCBI Gene Model | MGI Sequence Detail	604205	C57BL/6J
transcript	NM_177357	RefSeq | MGI Sequence Detail	15439	C57BL/6
polypeptide	A2CG49	UniProt | EBI | MGI Sequence Detail	2964	Not Applicable

Protein
Information

• UniProt
  9 Sequences
• Protein Ontology
  PR:000009238 kalirin
  (term hierarchy)
• PDB
  1WFW, 7UR2
• EC
  2.7.11.1
• InterPro Domains
  IPR001251 CRAL-TRIO lipid binding domain
  IPR036865 CRAL-TRIO lipid binding domain superfamily
  IPR035899 Dbl homology (DH) domain superfamily
  IPR000219 Dbl homology domain
  IPR003961 Fibronectin type III
  IPR036116 Fibronectin type III superfamily
  IPR003599 Immunoglobulin domain subtype
  IPR013098 Immunoglobulin I-set
  IPR007110 Immunoglobulin-like domain
  IPR036179 Immunoglobulin-like domain superfamily
  IPR013783 Immunoglobulin-like fold
  IPR003598 Immunoglobulin subtype 2
  IPR058918 Kalirin/TRIO-like, spectrin repeats
  IPR047054 Kalirin/Triple functional domain protein, pleckstrin homology (PH) domain 1
  IPR028570 Kalirin/Triple functional domain protein, SH3 domain 1
  IPR047053 Kalirin/Triple functional domain protein, SH3 domain 2
  IPR011993 PH-like domain superfamily
  IPR001849 Pleckstrin homology domain
  IPR017441 Protein kinase, ATP binding site
  IPR000719 Protein kinase domain
  IPR011009 Protein kinase-like domain superfamily
  IPR051336 Rho GTPase-activating Guanine Nucleotide Exchange Factors
  IPR008271 Serine/threonine-protein kinase, active site
  IPR001452 SH3 domain
  IPR036028 SH3-like domain superfamily
  IPR055251 SOS1/NGEF-like, PH domain
  IPR018159 Spectrin/alpha-actinin
  IPR002017 Spectrin repeat
• GlyGen
  A2CG49 4 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (1 site)

Molecular
Reagents

• All nucleic 24

  cDNA 23

  Other 1

  
  

  Microarray probesets 6

Other
Accession IDs

MGI:1919628, MGI:2146601, MGI:2443174

References

• Summaries
  All 80

  Developmental Gene Expression 4

  Gene Ontology 11

  Phenotypes 29
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:385797 Xia M, et al., A machine learning-based megakaryocyte identification system uncovers resident organs, markers, and functional diversity. Dev Cell. 2026 May 11;

TSS for Kalrn:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr140885	Chr16:34394291-34394306 (-)	-652 bp
Tssr140884	Chr16:34393896-34393924 (-)	-263 bp
Tssr140883	Chr16:34386877-34386880 (-)	6,768 bp
Tssr140882	Chr16:34362532-34362536 (-)	31,113 bp
Tssr140881	Chr16:34338558-34338570 (-)	55,083 bp
Tssr140880	Chr16:34334575-34334581 (-)	59,069 bp
Tssr140879	Chr16:34334545-34334554 (-)	59,097 bp
Tssr140878	Chr16:34334454-34334498 (-)	59,171 bp
Tssr140877	Chr16:34334433-34334449 (-)	59,206 bp
Tssr140876	Chr16:34334414-34334426 (-)	59,227 bp
Tssr140875	Chr16:34083581-34083619 (-)	310,047 bp
Tssr140874	Chr16:34083549-34083578 (-)	310,083 bp
Tssr140873	Chr16:34083446-34083469 (-)	310,189 bp
Tssr140872	Chr16:34083419-34083435 (-)	310,220 bp
Tssr140871	Chr16:34083396-34083408 (-)	310,245 bp
Tssr140870	Chr16:34083372-34083383 (-)	310,269 bp
Tssr140869	Chr16:34083315-34083342 (-)	310,318 bp
Tssr4858	Chr16:34083305-34083312 (-)	310,338 bp
Tssr140868	Chr16:34083264-34083290 (-)	310,370 bp
Tssr140867	Chr16:34083248-34083258 (-)	310,394 bp
Tssr140866	Chr16:34083200-34083211 (-)	310,441 bp
Tssr140865	Chr16:34076032-34076038 (-)	317,612 bp
Tssr140864	Chr16:34075799-34075810 (-)	317,842 bp
Tssr140863	Chr16:34059534-34059542 (-)	334,109 bp
Tssr140862	Chr16:34043559-34043568 (-)	350,083 bp
Tssr140861	Chr16:34025201-34025203 (-)	368,445 bp
Tssr140860	Chr16:34019797-34019828 (-)	373,834 bp
Tssr140859	Chr16:34012153-34012157 (-)	381,492 bp
Tssr140858	Chr16:33996182-33996200 (-)	397,456 bp
Tssr140857	Chr16:33916353-33916430 (-)	477,255 bp
Tssr140856	Chr16:33902263-33902308 (-)	491,361 bp
Tssr140855	Chr16:33902168-33902191 (-)	491,467 bp
Tssr140854	Chr16:33860654-33860666 (-)	532,987 bp
Tssr4857	Chr16:33854821-33854827 (-)	538,823 bp
Tssr140853	Chr16:33833810-33833814 (-)	559,835 bp