Lrrtm4 MGI Mouse Gene Detail - MGI:2389180 - leucine rich repeat transmembrane neuronal 4

Symbol

Lrrtm4
Name

leucine rich repeat transmembrane neuronal 4
Synonyms

7530419J18Rik

Feature Type

protein coding gene
IDs

MGI:2389180
NCBI Gene: 243499
Alliance

gene page
Transcription Start Sites

16 TSS

Sequence Map

Chr6:79995860-80787124 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 35.05 cM
Mapping Data

2 experiments

SNPs within 2kb

23824 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2389180	protein coding gene	Chr6:79995828-80787143 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0030900	protein coding gene	Chr6:80870302-81717044 (+)
A/J	MGP_AJ_G0030869	protein coding gene	Chr6:77759356-78555040 (+)
AKR/J	MGP_AKRJ_G0030797	protein coding gene	Chr6:79996562-80825855 (+)
BALB/cJ	MGP_BALBcJ_G0030879	protein coding gene	Chr6:77804285-78613765 (+)
C3H/HeJ	MGP_C3HHeJ_G0030831	protein coding gene	Chr6:103514972-104322517 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0031339	protein coding gene	Chr6:83058176-83923636 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028525	protein coding gene	Chr6:76340492-77090363 (+)
CAST/EiJ	MGP_CASTEiJ_G0029988	protein coding gene	Chr6:79965096-80809143 (+)
CBA/J	MGP_CBAJ_G0030566	protein coding gene	Chr6:86308509-87213208 (+)
DBA/2J	MGP_DBA2J_G0030719	protein coding gene	Chr6:77103555-77893700 (+)
FVB/NJ	MGP_FVBNJ_G0030672	protein coding gene	Chr6:76372830-77163603 (+)
LP/J	MGP_LPJ_G0030798	protein coding gene	Chr6:80827638-81680090 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0030708	protein coding gene	Chr6:90587884-91564897 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031363	protein coding gene	Chr6:79826262-80670752 (+)
PWK/PhJ	MGP_PWKPhJ_G0029703	protein coding gene	Chr6:76009053-76810924 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029531	protein coding gene	Chr6:78694022-79526703 (+)
WSB/EiJ	MGP_WSBEiJ_G0030069	protein coding gene	Chr6:80274636-81108106 (+)

Human Ortholog

LRRTM4, leucine rich repeat transmembrane neuronal 4

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LRRTM4, leucine rich repeat transmembrane neuronal 4
Links

HGNC:19411

NCBI Gene ID: 80059

neXtProt AC: NX_Q86VH4

UniProt: Q86VH4
Chr Location

2p12; chr2:76747685-77593319 (-) GRCh38

MGI Vertebrate Homology

Lrrtm4 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: LRRTM4
Gene Tree

Lrrtm4

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Phenotype Summary

4 phenotypes from 1 allele in 1 genetic background
12 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

7
Endonuclease-mediated

2
Gene trapped

2
Spontaneous

1
Targeted

2
Genomic Mutations

2 involving Lrrtm4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

30 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit impaired excitatory synapse development and excitatory transmission in dentate gyrus granule cells.

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All GO Annotations

20
GO References

9

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

827
Tissues

38
cDNA Data

7
Literature Summary

5

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lrrtm4

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All Sequences

74
RefSeq

22
UniProt

6
CCDS

CCDS20259.2, CCDS71778.1, CCDS71779.1, CCDS90065.1

Ensembl

ENSMUSG00000052581 (Evidence)
NCBI Gene

243499

			Length	Strain/Species	Flank
genomic	ENSMUSG00000052581	Ensembl Gene Model \| MGI Sequence Detail	791265	C57BL/6J	± kb
transcript	ENSMUST00000147663	Ensembl \| MGI Sequence Detail	3033	Not Applicable
polypeptide	ENSMUSP00000117263	Ensembl \| MGI Sequence Detail	591	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000009949 leucine-rich repeat transmembrane neuronal protein 4

(term hierarchy)
InterPro Domains

IPR001611 Leucine-rich repeat

IPR032675 Leucine-rich repeat domain superfamily

IPR003591 Leucine-rich repeat, typical subtype

IPR050328 Multifunctional Developmental and Immune Receptor

IPR050333 Small Leucine-Rich Proteoglycans
GlyGen

Q80XG9 5 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (2 sites)

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All nucleic 7

cDNA 7

Microarray probesets 4

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MGI:2445039

Summaries

All 37

Developmental Gene Expression 5

Gene Ontology 9

Phenotypes 12
Earliest

J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
Latest

J:326541 Cyagen Biosciences Inc., Cyagen Biosciences Website. 2022;

TSS for Lrrtm4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr57230	Chr6:79995888-79995928 (+)	48 bp
Tssr57231	Chr6:79995940-79995980 (+)	100 bp
Tssr57232	Chr6:79995991-79996013 (+)	142 bp
Tssr57233	Chr6:79996051-79996062 (+)	197 bp
Tssr57234	Chr6:80045025-80045028 (+)	49,167 bp
Tssr57235	Chr6:80047693-80047724 (+)	51,849 bp
Tssr57237	Chr6:80150778-80150790 (+)	154,924 bp
Tssr57238	Chr6:80151063-80151072 (+)	155,208 bp
Tssr57239	Chr6:80151086-80151095 (+)	155,231 bp
Tssr57240	Chr6:80169549-80169555 (+)	173,692 bp
Tssr57241	Chr6:80191736-80191767 (+)	195,892 bp
Tssr57242	Chr6:80291434-80291443 (+)	295,579 bp
Tssr57243	Chr6:80378588-80378595 (+)	382,732 bp
Tssr57244	Chr6:80435729-80435730 (+)	439,870 bp
Tssr57246	Chr6:80543133-80543137 (+)	547,275 bp
Tssr57247	Chr6:80786553-80786587 (+)	790,710 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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