Lrrc39 Gene Detail

Summary

• Symbol
  Lrrc39
• Name
  leucine rich repeat containing 39
• Synonyms
  2010005E21Rik, 9430028I06Rik, Myomasp

• Feature Type
  protein coding gene
• IDs
  MGI:1924557
  NCBI Gene: 109245
• Alliance
  gene page
• Transcription Start Sites
  5 TSS

Location &
Maps

• Sequence Map
  Chr3:116356622-116376783 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 3, 50.39 cM, cytoband G2
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  182 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924557	protein coding gene	Chr3:116356610-116376793 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027812	protein coding gene	Chr3:118466323-118486480 (+)
A/J	MGP_AJ_G0027770	protein coding gene	Chr3:114589822-114610773 (+)
AKR/J	MGP_AKRJ_G0027736	protein coding gene	Chr3:117497334-117517482 (+)
BALB/cJ	MGP_BALBcJ_G0027782	protein coding gene	Chr3:114433062-114453356 (+)
C3H/HeJ	MGP_C3HHeJ_G0027513	protein coding gene	Chr3:117848288-117876867 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028228	protein coding gene	Chr3:122814221-122835984 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025567	protein coding gene	Chr3:110281194-110301789 (+)
CAST/EiJ	MGP_CASTEiJ_G0026969	protein coding gene	Chr3:117140123-117161797 (+)
CBA/J	MGP_CBAJ_G0027488	protein coding gene	Chr3:127010319-127030445 (+)
DBA/2J	MGP_DBA2J_G0027629	protein coding gene	Chr3:113820560-113840710 (+)
FVB/NJ	MGP_FVBNJ_G0027597	protein coding gene	Chr3:111463938-111484788 (+)
LP/J	MGP_LPJ_G0027739	protein coding gene	Chr3:120009662-120029803 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027627	protein coding gene	Chr3:134392774-134414329 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028284	protein coding gene	Chr3:117021691-117043813 (+)
PWK/PhJ	MGP_PWKPhJ_G0026695	protein coding gene	Chr3:113472312-113492747 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026517	protein coding gene	Chr3:115042567-115063315 (+)
WSB/EiJ	MGP_WSBEiJ_G0027049	protein coding gene	Chr3:117710623-117734141 (+)

Homology

• Human Ortholog
  LRRC39, leucine rich repeat containing 39

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  LRRC39, leucine rich repeat containing 39
  
• Links
  HGNC:28228

  NCBI Gene ID: 127495

  neXtProt AC: NX_Q96DD0

  UniProt: Q96DD0

  
  
• Chr Location
  1p21.2; chr1:100148448-100178273 (-)  GRCh38.p7

---

• Alliance of Genome Resources
  Lrrc39 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: LRRC39
• Gene Tree
  Lrrc39
  

Human Diseases

• References
  1 with disease annotations

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  7 phenotype references
  

• All Mutations and Alleles
  4
• Chemically induced (other)
  1
• Radiation induced
  1
• Targeted
  2
• Genomic Mutations
  2 involving Lrrc39
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  15 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  1
• GO References
  1

Expression

• Assay Results
  706
• cDNA Data
  14

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase lrrc39

Interactions

• Lrrc39 interacts with 294 markers (Mir7-1, Mir7-2, Mir9-1, ...) View All

Sequences &
Gene Models

• All Sequences
  50
• RefSeq
  11
• UniProt
  3
• CCDS
  CCDS17788.1

• Ensembl
  ENSMUSG00000027961 (Evidence)
• NCBI Gene
  109245

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000027961	Ensembl Gene Model | MGI Sequence Detail	20162	C57BL/6J
transcript	ENSMUST00000029573	Ensembl | MGI Sequence Detail	3087	Not Applicable
polypeptide	ENSMUSP00000029573	Ensembl | MGI Sequence Detail	337	Not Applicable

Protein
Information

• UniProt
  3 Sequences
• Protein Ontology
  PR:000031360 leucine-rich repeat-containing protein 39
  (term hierarchy)
• InterPro Domains
  IPR001611 Leucine-rich repeat
  IPR032675 Leucine-rich repeat domain superfamily
  IPR003591 Leucine-rich repeat, typical subtype

Molecular
Reagents

• All nucleic 14

  cDNA 14

  
  

  Microarray probesets 5

Other
Accession IDs

MGI:1917361

References

• Summaries
  All 26

  Diseases 1

  Gene Ontology 1

  Phenotypes 7
• 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:302829 Lu J, et al., Mouse models for human hyperuricaemia: a critical review. Nat Rev Rheumatol. 2019 Jul;15(7):413-426

TSS for Lrrc39:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr31355	Chr3:116356592-116356613 (+)	-19 bp
Tssr31356	Chr3:116356614-116356653 (+)	12 bp
Tssr31357	Chr3:116356657-116356676 (+)	45 bp
Tssr31358	Chr3:116356700-116356712 (+)	84 bp
Tssr31359	Chr3:116356713-116356737 (+)	103 bp