Lrit1 MGI Mouse Gene Detail - MGI:2385320 - leucine-rich repeat, immunoglobulin-like and transmembrane domains 1

Symbol

Lrit1
Name

leucine-rich repeat, immunoglobulin-like and transmembrane domains 1
Synonyms

Lrrc21, MGC:40670

Feature Type

protein coding gene
IDs

MGI:2385320
NCBI Gene: 239037
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr14:36776787-36786903 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 14, 21.29 cM
Mapping Data

1 experiment

SNPs within 2kb

408 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2385320	protein coding gene	Chr14:36764432-36786903 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0021185	protein coding gene	Chr14:30555023-30565914 (+)
A/J	MGP_AJ_G0021133	protein coding gene	Chr14:29277534-29300630 (+)
AKR/J	MGP_AKRJ_G0021110	protein coding gene	Chr14:30626769-30638599 (+)
BALB/cJ	MGP_BALBcJ_G0021137	protein coding gene	Chr14:29521176-29532273 (+)
C3H/HeJ	MGP_C3HHeJ_G0020920	protein coding gene	Chr14:30510318-30520776 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0021569	protein coding gene	Chr14:31652706-31662492 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0019131	protein coding gene	Chr14:29275320-29285081 (+)
CAST/EiJ	MGP_CASTEiJ_G0020445	protein coding gene	Chr14:30383588-30407488 (+)
CBA/J	MGP_CBAJ_G0020886	protein coding gene	Chr14:32831217-32843240 (+)
DBA/2J	MGP_DBA2J_G0021009	protein coding gene	Chr14:29326840-29341735 (+)
FVB/NJ	MGP_FVBNJ_G0020993	protein coding gene	Chr14:29308954-29318744 (+)
LP/J	MGP_LPJ_G0021078	protein coding gene	Chr14:30849784-30859547 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0021019	protein coding gene	Chr14:32023321-32046245 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0021602	protein coding gene	Chr14:30488552-30500524 (+)
PWK/PhJ	MGP_PWKPhJ_G0020193	protein coding gene	Chr14:28860608-28884612 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0020017	protein coding gene	Chr14:30025130-30047873 (+)
WSB/EiJ	MGP_WSBEiJ_G0020500	protein coding gene	Chr14:30517046-30526833 (+)

Human Ortholog

LRIT1, leucine rich repeat, Ig-like and transmembrane domains 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LRIT1, leucine rich repeat, Ig-like and transmembrane domains 1
Synonyms

FIGLER9, LRRC21, PAL
Links

HGNC:23404

NCBI Gene ID: 26103

neXtProt AC: NX_Q9P2V4

UniProt: Q9P2V4
Chr Location

10q23.1; chr10:84231520-84241546 (-) GRCh38

MGI Vertebrate Homology

Lrit1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LRIT1
Gene Tree

Lrit1

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Phenotype Summary

3 phenotypes from 1 allele in 1 genetic background
3 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

4
Targeted

4
Genomic Mutations

1 involving Lrit1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

38 strains or lines available

Mice homozygous for a knock-out allele exhibit impaired synaptic communication of cone photoreceptors.

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All GO Annotations

5
GO References

4

Molecular Function

No experimental evidence to support Molecular Function annotation, following literature review. See J:73796.

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

719
Tissues

13
cDNA Data

12
Literature Summary

3

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lrit1

ZFIN lrit1b

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All Sequences

31
RefSeq

4
UniProt

1
CCDS

CCDS26950.2

Ensembl

ENSMUSG00000041044 (Evidence)
NCBI Gene

239037

			Length	Strain/Species	Flank
genomic	ENSMUSG00000041044	Ensembl Gene Model \| MGI Sequence Detail	10117	C57BL/6J	± kb
transcript	ENSMUST00000120052	Ensembl \| MGI Sequence Detail	4325	Not Applicable
polypeptide	ENSMUSP00000113964	Ensembl \| MGI Sequence Detail	624	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000009915 leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 1

(term hierarchy)
InterPro Domains

IPR000483 Cysteine-rich flanking region, C-terminal

IPR003961 Fibronectin type III

IPR036116 Fibronectin type III superfamily

IPR013098 Immunoglobulin I-set

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR003599 Immunoglobulin subtype

IPR003598 Immunoglobulin subtype 2

IPR001611 Leucine-rich repeat

IPR050467 Leucine-rich repeat and fibronectin type-III domain-containing

IPR032675 Leucine-rich repeat domain superfamily

IPR000372 Leucine-rich repeat N-terminal domain

IPR003591 Leucine-rich repeat, typical subtype
GlyGen

Q8K099 3 sites

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All nucleic 14

cDNA 12

Primer pair 1

Other 1

Microarray probesets 3

Summaries

All 29

Developmental Gene Expression 3

Gene Ontology 4

Phenotypes 3
Earliest

J:82808 Strausberg RL, et al., Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903
Latest

J:271244 Ueno A, et al., Lrit1, a Retinal Transmembrane Protein, Regulates Selective Synapse Formation in Cone Photoreceptor Cells and Visual Acuity. Cell Rep. 2018 Mar 27;22(13):3548-3561

TSS for Lrit1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr125113	Chr14:36776775-36776810 (+)	6 bp
Tssr125114	Chr14:36776816-36776819 (+)	31 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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