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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

Might facilitate FGFR1 exit from the endoplasmic reticulum to the Golgi. Could be a regulator of the FGFRs.1 Publication

GO - Biological processi

Complete GO annotation...

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)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei583 – 60321HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti328 – 3281C → Y in CSNB1F. 1 Publication
VAR_069746

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi53 – 531T → M: No effect on LRIT3 function. 1 Publication

Keywords - Diseasei

Congenital stationary night blindness, Disease mutation

Organism-specific databases

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

Polymorphism and mutation databases

DMDMi476007838.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1919Sequence analysisAdd
BLAST
Chaini20 – 679660Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3PRO_0000309284Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi275 ↔ 328PROSITE-ProRule annotation
Glycosylationi296 – 2961N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

Glycosylated.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ3SXY7.
PRIDEiQ3SXY7.

PTM databases

PhosphoSiteiQ3SXY7.

Expressioni

Gene expression databases

BgeeiQ3SXY7.
CleanExiHS_LRIT3.
ExpressionAtlasiQ3SXY7. baseline and differential.

Organism-specific databases

HPAiHPA013454.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000369252.

Structurei

3D structure databases

ProteinModelPortaliQ3SXY7.
SMRiQ3SXY7. Positions 21-348.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati56 – 7924LRR 1Add
BLAST
Repeati80 – 10324LRR 2Add
BLAST
Repeati104 – 12825LRR 3Add
BLAST
Repeati129 – 15123LRR 4Add
BLAST
Repeati152 – 17524LRR 5Add
BLAST
Domaini201 – 25353LRRCTAdd
BLAST
Domaini254 – 34491Ig-likeAdd
BLAST
Domaini486 – 57489Fibronectin type-IIIPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi373 – 43361Ser-richAdd
BLAST

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.
GeneTreeiENSGT00840000129760.
HOGENOMiHOG000063714.
HOVERGENiHBG108105.
InParanoidiQ3SXY7.
OMAiSIDSQMT.
OrthoDBiEOG7D2FD8.
TreeFamiTF330861.

Family and domain databases

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 AAI04038.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti169 – 1691P → T in AAI04038 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti175 – 1751S → N.1 Publication
Corresponds to variant rs4698797 [ dbSNP | Ensembl ].
VAR_061317
Natural varianti328 – 3281C → Y in CSNB1F. 1 Publication
VAR_069746
Natural varianti336 – 3361M → L.2 Publications
Corresponds to variant rs764205 [ dbSNP | Ensembl ].
VAR_036927
Natural varianti486 – 4861A → T.1 Publication
Corresponds to variant rs2347131 [ dbSNP | Ensembl ].
VAR_036928
Natural varianti494 – 4941S → T in one non-syndromic craniosynostosis patient; unknown pathological significance. 1 Publication
VAR_069133
Natural varianti503 – 5031T → M.1 Publication
Corresponds to variant rs2347132 [ dbSNP | Ensembl ].
VAR_036929
Natural varianti592 – 5921C → Y Found in a patient with non-syndromic craniosynostosis; unknown pathological significance. 1 Publication
VAR_069134

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei46 – 183138Missing in isoform 2. 1 PublicationVSP_029126Add
BLAST
Alternative sequencei184 – 19613SGVLD…SRIIL → MVEPHQEPRHSKV in isoform 2. 1 PublicationVSP_029127Add
BLAST

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.
SMRiQ3SXY7. Positions 21-348.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000369252.

PTM databases

PhosphoSiteiQ3SXY7.

Polymorphism and mutation databases

DMDMi476007838.

Proteomic databases

PaxDbiQ3SXY7.
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.
GeneCardsiLRIT3.
HGNCiHGNC:24783. LRIT3.
HPAiHPA013454.
MalaCardsiLRIT3.
MIMi615004. gene.
615058. phenotype.
neXtProtiNX_Q3SXY7.
Orphaneti215. Congenital stationary night blindness.
PharmGKBiPA162394355.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0619. Eukaryota.
KOG3510. Eukaryota.
ENOG4110XFB. LUCA.
GeneTreeiENSGT00840000129760.
HOGENOMiHOG000063714.
HOVERGENiHBG108105.
InParanoidiQ3SXY7.
OMAiSIDSQMT.
OrthoDBiEOG7D2FD8.
TreeFamiTF330861.

Miscellaneous databases

GenomeRNAii345193.
NextBioi98830.
PROiQ3SXY7.
SOURCEiSearch...

Gene expression databases

BgeeiQ3SXY7.
CleanExiHS_LRIT3.
ExpressionAtlasiQ3SXY7. baseline and differential.

Family and domain databases

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...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT LEU-336.
    Tissue: Cerebellum.
  2. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT LEU-336.
  4. "Leucine-rich repeat, immunoglobulin-like and transmembrane domain 3 (LRIT3) is a modulator of FGFR1."
    Kim S.D., Liu J.L., Roscioli T., Buckley M.F., Yagnik G., Boyadjiev S.A., Kim J.
    FEBS Lett. 586:1516-1521(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-83, IDENTIFICATION OF EXON 1, FUNCTION, GLYCOSYLATION, VARIANTS THR-494 AND TYR-592, MUTAGENESIS OF THR-53.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 108-634 (ISOFORM 1), VARIANTS ASN-175; THR-486 AND MET-503.
  6. Cited for: VARIANT CSNB1F TYR-328.

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: May 11, 2016
This is version 107 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.