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Protein

Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3

Gene

LRIT3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required in retinal ON-bipolar cells for normal localization of the cation channel TRPM1 at dendrite tips (By similarity). May also have a role in cone synapse formation (By similarity). Might facilitate FGFR1 exit from the endoplasmic reticulum to the Golgi (PubMed:22673519). Could be a regulator of the FGFRs (PubMed:22673519).By similarity1 Publication

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Sensory transduction, Vision

Enzyme and pathway databases

BioCyciZFISH:G66-31361-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3
Gene namesi
Name:LRIT3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:24783. LRIT3.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini20 – 582LumenalCuratedAdd BLAST563
Transmembranei583 – 603HelicalSequence analysisAdd BLAST21
Topological domaini604 – 679CytoplasmicCuratedAdd BLAST76

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Endoplasmic reticulum, Membrane

Pathology & Biotechi

Involvement in diseasei

Night blindness, congenital stationary, 1F (CSNB1F)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia.
See also OMIM:615058
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_069746328C → Y in CSNB1F. 1 PublicationCorresponds to variant rs376610215dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi53T → M: No effect on LRIT3 function. 1 Publication1

Keywords - Diseasei

Congenital stationary night blindness, Disease mutation

Organism-specific databases

DisGeNETi345193.
MalaCardsiLRIT3.
MIMi615058. phenotype.
OpenTargetsiENSG00000183423.
Orphaneti215. Congenital stationary night blindness.
PharmGKBiPA162394355.

Polymorphism and mutation databases

DMDMi476007838.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Sequence analysisAdd BLAST19
ChainiPRO_000030928420 – 679Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3Add BLAST660

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi275 ↔ 328PROSITE-ProRule annotation
Glycosylationi296N-linked (GlcNAc...)Sequence analysis1

Post-translational modificationi

Glycosylated.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ3SXY7.
PeptideAtlasiQ3SXY7.
PRIDEiQ3SXY7.

PTM databases

iPTMnetiQ3SXY7.
PhosphoSitePlusiQ3SXY7.

Expressioni

Tissue specificityi

Detected in the outer plexiform layer (OPL) of the retina where it localizes to ON-bipolar cells (at protein level).1 Publication

Gene expression databases

BgeeiENSG00000183423.
CleanExiHS_LRIT3.
ExpressionAtlasiQ3SXY7. baseline and differential.

Organism-specific databases

HPAiHPA013454.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000369252.

Structurei

3D structure databases

ProteinModelPortaliQ3SXY7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati56 – 79LRR 1Add BLAST24
Repeati80 – 103LRR 2Add BLAST24
Repeati104 – 128LRR 3Add BLAST25
Repeati129 – 151LRR 4Add BLAST23
Repeati152 – 175LRR 5Add BLAST24
Domaini201 – 253LRRCTAdd BLAST53
Domaini254 – 344Ig-likeAdd BLAST91
Domaini486 – 574Fibronectin type-IIIPROSITE-ProRule annotationAdd BLAST89

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi373 – 433Ser-richAdd BLAST61

Sequence similaritiesi

Contains 1 fibronectin type-III domain.PROSITE-ProRule annotation
Contains 5 LRR (leucine-rich) repeats.Curated
Contains 1 LRRCT domain.Curated

Keywords - Domaini

Immunoglobulin domain, Leucine-rich repeat, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
KOG3510. Eukaryota.
ENOG4110XFB. LUCA.
GeneTreeiENSGT00850000132257.
HOGENOMiHOG000063714.
HOVERGENiHBG108105.
InParanoidiQ3SXY7.
OMAiSIDSQMT.
OrthoDBiEOG091G0ACR.
TreeFamiTF330861.

Family and domain databases

CDDicd00063. FN3. 1 hit.
Gene3Di2.60.40.10. 2 hits.
3.80.10.10. 1 hit.
InterProiIPR003961. FN3_dom.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
[Graphical view]
PfamiPF13855. LRR_8. 2 hits.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00369. LRR_TYP. 4 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF49265. SSF49265. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50853. FN3. 1 hit.
PS50835. IG_LIKE. 1 hit.
PS51450. LRR. 4 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q3SXY7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MHLFACLCIV LSFLEGVGCL CPSQCTCDYH GRNDGSGSRL VLCNDMDMNE
60 70 80 90 100
LPTNLPVDTV KLRIEKTVIR RISAEAFYYL VELQYLWVTY NSVASIDPSS
110 120 130 140 150
FYNLKQLHEL RLDGNSLAAF PWASLLDMPL LRTLDLHNNK ITSVPNEALR
160 170 180 190 200
YLKNLAYLDL SSNRLTTLPP DFLESWTHLV STPSGVLDLS PSRIILGLQD
210 220 230 240 250
NPWFCDCHIS KMIELSKVVD PAIVLLDPLM TCSEPERLTG ILFQRAELEH
260 270 280 290 300
CLKPSVMTSA TKIMSALGSN VLLRCDATGF PTPQITWTRS DSSPVNYTVI
310 320 330 340 350
QESPEEGVRW SIMSLTGISS KDAGDYKCKA KNLAGMSEAV VTVTVLGITT
360 370 380 390 400
TPIPPDTSER TGDHPEWDVQ PGSGRSTSVS SASSYLWSSS FSPTSSFSAS
410 420 430 440 450
TLSPPSTASF SLSPFSSSTV SSTTTLSTSI SASTTMANKR SFQLHQGGKR
460 470 480 490 500
NLKVAKNGSK LPPASTSKKE ELALLDQTML TETNAAIENL RVVSETKESV
510 520 530 540 550
TLTWNMINTT HNSAVTVLYS KYGGKDLLLL NADSSKNQVT IDGLEPGGQY
560 570 580 590 600
MACVCPKGVP PQKDQCITFS TERVEGDDSQ WSLLLVVTST ACVVILPLIC
610 620 630 640 650
FLLYKVCKLQ CKSEPFWEDD LAKETYIQFE TLFPRSQSVG ELWTRSHRDD
660 670
SEKLLLCSRS SVESQVTFKS EGSRPEYYC
Note: No experimental confirmation available.
Length:679
Mass (Da):74,754
Last modified:April 3, 2013 - v3
Checksum:i76CADAE7080021E5
GO
Isoform 2 (identifier: Q3SXY7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     46-183: Missing.
     184-196: SGVLDLSPSRIIL → MVEPHQEPRHSKV

Note: No experimental confirmation available.
Show »
Length:541
Mass (Da):59,051
Checksum:i4363DEA8D464A387
GO

Sequence cautioni

The sequence AAI04038 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti169P → T in AAI04038 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_061317175S → N.1 PublicationCorresponds to variant rs4698797dbSNPEnsembl.1
Natural variantiVAR_069746328C → Y in CSNB1F. 1 PublicationCorresponds to variant rs376610215dbSNPEnsembl.1
Natural variantiVAR_036927336M → L.2 PublicationsCorresponds to variant rs764205dbSNPEnsembl.1
Natural variantiVAR_036928486A → T.1 PublicationCorresponds to variant rs2347131dbSNPEnsembl.1
Natural variantiVAR_069133494S → T in one non-syndromic craniosynostosis patient; unknown pathological significance. 1 Publication1
Natural variantiVAR_036929503T → M.1 PublicationCorresponds to variant rs2347132dbSNPEnsembl.1
Natural variantiVAR_069134592C → Y Found in a patient with non-syndromic craniosynostosis; unknown pathological significance. 1 PublicationCorresponds to variant rs766899767dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_02912646 – 183Missing in isoform 2. 1 PublicationAdd BLAST138
Alternative sequenceiVSP_029127184 – 196SGVLD…SRIIL → MVEPHQEPRHSKV in isoform 2. 1 PublicationAdd BLAST13

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK126648 mRNA. Translation: BAC86628.1.
AC005509 Genomic DNA. No translation available.
CH471057 Genomic DNA. Translation: EAX06256.1.
JQ354981 mRNA. Translation: AFH56665.1.
BC104037 mRNA. Translation: AAI04038.1. Different initiation.
CCDSiCCDS3688.3. [Q3SXY7-1]
RefSeqiNP_940908.3. NM_198506.4. [Q3SXY7-1]
UniGeneiHs.308127.

Genome annotation databases

EnsembliENST00000594814; ENSP00000469759; ENSG00000183423. [Q3SXY7-1]
GeneIDi345193.
KEGGihsa:345193.
UCSCiuc031sgv.2. human. [Q3SXY7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK126648 mRNA. Translation: BAC86628.1.
AC005509 Genomic DNA. No translation available.
CH471057 Genomic DNA. Translation: EAX06256.1.
JQ354981 mRNA. Translation: AFH56665.1.
BC104037 mRNA. Translation: AAI04038.1. Different initiation.
CCDSiCCDS3688.3. [Q3SXY7-1]
RefSeqiNP_940908.3. NM_198506.4. [Q3SXY7-1]
UniGeneiHs.308127.

3D structure databases

ProteinModelPortaliQ3SXY7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000369252.

PTM databases

iPTMnetiQ3SXY7.
PhosphoSitePlusiQ3SXY7.

Polymorphism and mutation databases

DMDMi476007838.

Proteomic databases

PaxDbiQ3SXY7.
PeptideAtlasiQ3SXY7.
PRIDEiQ3SXY7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000594814; ENSP00000469759; ENSG00000183423. [Q3SXY7-1]
GeneIDi345193.
KEGGihsa:345193.
UCSCiuc031sgv.2. human. [Q3SXY7-1]

Organism-specific databases

CTDi345193.
DisGeNETi345193.
GeneCardsiLRIT3.
HGNCiHGNC:24783. LRIT3.
HPAiHPA013454.
MalaCardsiLRIT3.
MIMi615004. gene.
615058. phenotype.
neXtProtiNX_Q3SXY7.
OpenTargetsiENSG00000183423.
Orphaneti215. Congenital stationary night blindness.
PharmGKBiPA162394355.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
KOG3510. Eukaryota.
ENOG4110XFB. LUCA.
GeneTreeiENSGT00850000132257.
HOGENOMiHOG000063714.
HOVERGENiHBG108105.
InParanoidiQ3SXY7.
OMAiSIDSQMT.
OrthoDBiEOG091G0ACR.
TreeFamiTF330861.

Enzyme and pathway databases

BioCyciZFISH:G66-31361-MONOMER.

Miscellaneous databases

GenomeRNAii345193.
PROiQ3SXY7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000183423.
CleanExiHS_LRIT3.
ExpressionAtlasiQ3SXY7. baseline and differential.

Family and domain databases

CDDicd00063. FN3. 1 hit.
Gene3Di2.60.40.10. 2 hits.
3.80.10.10. 1 hit.
InterProiIPR003961. FN3_dom.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
[Graphical view]
PfamiPF13855. LRR_8. 2 hits.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00369. LRR_TYP. 4 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF49265. SSF49265. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50853. FN3. 1 hit.
PS50835. IG_LIKE. 1 hit.
PS51450. LRR. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLRIT3_HUMAN
AccessioniPrimary (citable) accession number: Q3SXY7
Secondary accession number(s): C9J1C2, Q6ZTG1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: April 3, 2013
Last modified: November 30, 2016
This is version 113 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.