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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: -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

Keywordsi

Biological processSensory transduction, Vision

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

EuPathDBiHostDB:ENSG00000183423.11
HGNCiHGNC:24783 LRIT3
MIMi615004 gene
neXtProtiNX_Q3SXY7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

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 dbSNP:rs376610215EnsemblClinVar.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...) asparagineSequence analysis1

Post-translational modificationi

Glycosylated.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ3SXY7
PeptideAtlasiQ3SXY7
PRIDEiQ3SXY7
ProteomicsDBi61821
61822 [Q3SXY7-2]

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 Expressed in 63 organ(s), highest expression level in caudate nucleus
CleanExiHS_LRIT3
ExpressionAtlasiQ3SXY7 baseline and differential

Organism-specific databases

HPAiHPA013454

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000369252

Structurei

3D structure databases

ProteinModelPortaliQ3SXY7
SMRiQ3SXY7
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

Keywords - Domaini

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

Phylogenomic databases

eggNOGiKOG0619 Eukaryota
KOG3510 Eukaryota
ENOG4110XFB LUCA
GeneTreeiENSGT00920000149011
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
InterProiView protein in InterPro
IPR003961 FN3_dom
IPR036116 FN3_sf
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
IPR003598 Ig_sub2
IPR001611 Leu-rich_rpt
IPR003591 Leu-rich_rpt_typical-subtyp
IPR032675 LRR_dom_sf
PfamiView protein in Pfam
PF13855 LRR_8, 2 hits
SMARTiView protein in SMART
SM00409 IG, 1 hit
SM00408 IGc2, 1 hit
SM00369 LRR_TYP, 4 hits
SUPFAMiSSF48726 SSF48726, 1 hit
SSF49265 SSF49265, 1 hit
PROSITEiView protein in PROSITE
PS50853 FN3, 1 hit
PS50835 IG_LIKE, 1 hit
PS51450 LRR, 4 hits

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

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A0A0MR64A0A0A0MR64_HUMAN
Leucine-rich repeat, immunoglobulin...
LRIT3
496Annotation score:

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 → N1 PublicationCorresponds to variant dbSNP:rs4698797EnsemblClinVar.1
Natural variantiVAR_069746328C → Y in CSNB1F. 1 PublicationCorresponds to variant dbSNP:rs376610215EnsemblClinVar.1
Natural variantiVAR_036927336M → L2 PublicationsCorresponds to variant dbSNP:rs764205EnsemblClinVar.1
Natural variantiVAR_036928486A → T1 PublicationCorresponds to variant dbSNP:rs2347131EnsemblClinVar.1
Natural variantiVAR_069133494S → T in one non-syndromic craniosynostosis patient; unknown pathological significance. 1 Publication1
Natural variantiVAR_036929503T → M1 PublicationCorresponds to variant dbSNP:rs2347132EnsemblClinVar.1
Natural variantiVAR_069134592C → Y Found in a patient with non-syndromic craniosynostosis; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs766899767Ensembl.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

Similar proteinsi

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
SMRiQ3SXY7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000369252

PTM databases

iPTMnetiQ3SXY7
PhosphoSitePlusiQ3SXY7

Polymorphism and mutation databases

DMDMi476007838

Proteomic databases

PaxDbiQ3SXY7
PeptideAtlasiQ3SXY7
PRIDEiQ3SXY7
ProteomicsDBi61821
61822 [Q3SXY7-2]

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
EuPathDBiHostDB:ENSG00000183423.11
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
GeneTreeiENSGT00920000149011
HOGENOMiHOG000063714
HOVERGENiHBG108105
InParanoidiQ3SXY7
OMAiSIDSQMT
OrthoDBiEOG091G0ACR
TreeFamiTF330861

Miscellaneous databases

GenomeRNAii345193
PROiPR:Q3SXY7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000183423 Expressed in 63 organ(s), highest expression level in caudate nucleus
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
InterProiView protein in InterPro
IPR003961 FN3_dom
IPR036116 FN3_sf
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
IPR003598 Ig_sub2
IPR001611 Leu-rich_rpt
IPR003591 Leu-rich_rpt_typical-subtyp
IPR032675 LRR_dom_sf
PfamiView protein in Pfam
PF13855 LRR_8, 2 hits
SMARTiView protein in SMART
SM00409 IG, 1 hit
SM00408 IGc2, 1 hit
SM00369 LRR_TYP, 4 hits
SUPFAMiSSF48726 SSF48726, 1 hit
SSF49265 SSF49265, 1 hit
PROSITEiView protein in PROSITE
PS50853 FN3, 1 hit
PS50835 IG_LIKE, 1 hit
PS51450 LRR, 4 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLRIT3_HUMAN
AccessioniPrimary (citable) accession number: Q3SXY7
Secondary accession number(s): C9J1C2, Q6ZTG1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: April 3, 2013
Last modified: September 12, 2018
This is version 124 of the entry and version 3 of the sequence. See 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
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