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Protein

Leucine-rich repeat and calponin homology domain-containing protein 1

Gene

LRCH1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Names & Taxonomyi

Protein namesi
Recommended name:
Leucine-rich repeat and calponin homology domain-containing protein 1
Alternative name(s):
Calponin homology domain-containing protein 1
Neuronal protein 81
Short name:
NP81
Gene namesi
Name:LRCH1
Synonyms:CHDC1, KIAA1016
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:20309. LRCH1.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134898200.

Polymorphism and mutation databases

BioMutaiLRCH1.
DMDMi296439310.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 728728Leucine-rich repeat and calponin homology domain-containing protein 1PRO_0000084478Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei370 – 3701PhosphoserineCombined sources
Modified residuei409 – 4091PhosphoserineBy similarity
Modified residuei532 – 5321PhosphoserineBy similarity
Modified residuei536 – 5361PhosphoserineBy similarity
Modified residuei568 – 5681PhosphothreonineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9Y2L9.
MaxQBiQ9Y2L9.
PaxDbiQ9Y2L9.
PRIDEiQ9Y2L9.

PTM databases

iPTMnetiQ9Y2L9.
PhosphoSiteiQ9Y2L9.

Expressioni

Gene expression databases

BgeeiQ9Y2L9.
CleanExiHS_LRCH1.
ExpressionAtlasiQ9Y2L9. baseline and differential.
GenevisibleiQ9Y2L9. HS.

Organism-specific databases

HPAiHPA021536.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
DOCK8Q8NF50-25EBI-2797324,EBI-10174653

Protein-protein interaction databases

BioGridi116760. 11 interactions.
IntActiQ9Y2L9. 10 interactions.
STRINGi9606.ENSP00000374447.

Structurei

3D structure databases

ProteinModelPortaliQ9Y2L9.
SMRiQ9Y2L9. Positions 63-275.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati98 – 11922LRR 1Add
BLAST
Repeati121 – 14323LRR 2Add
BLAST
Repeati144 – 16623LRR 3Add
BLAST
Repeati167 – 18721LRR 4Add
BLAST
Repeati189 – 21022LRR 5Add
BLAST
Repeati212 – 23423LRR 6Add
BLAST
Repeati235 – 25521LRR 7Add
BLAST
Repeati257 – 27822LRR 8Add
BLAST
Repeati283 – 30422LRR 9Add
BLAST
Domaini576 – 689114CHPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi21 – 3616His-richAdd
BLAST
Compositional biasi37 – 5418Gly-richAdd
BLAST

Sequence similaritiesi

Contains 1 CH (calponin-homology) domain.PROSITE-ProRule annotation
Contains 9 LRR (leucine-rich) repeats.Curated

Keywords - Domaini

Leucine-rich repeat, Repeat

Phylogenomic databases

eggNOGiKOG0532. Eukaryota.
KOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00840000129676.
HOGENOMiHOG000049055.
HOVERGENiHBG052350.
InParanoidiQ9Y2L9.
OMAiRHIRKTV.
OrthoDBiEOG7288QT.
PhylomeDBiQ9Y2L9.
TreeFamiTF318428.

Family and domain databases

Gene3Di1.10.418.10. 1 hit.
3.80.10.10. 1 hit.
InterProiIPR001715. CH-domain.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
[Graphical view]
PfamiPF00307. CH. 1 hit.
PF13855. LRR_8. 2 hits.
[Graphical view]
SMARTiSM00033. CH. 1 hit.
SM00369. LRR_TYP. 5 hits.
[Graphical view]
SUPFAMiSSF47576. SSF47576. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50021. CH. 1 hit.
PS51450. LRR. 6 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y2L9-1) [UniParc]FASTAAdd to basket

Also known as: b, NP81b

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
MATPGSEPQP FVPALSVATL HPLHHPHHHH HHHQHHGGTG APGGAGGGGG
60 70 80 90 100
GSGGFNLPLN RGLERALEEA ANSGGLNLSA RKLKEFPRTA APGHDLSDTV
110 120 130 140 150
QADLSKNRLV EVPMELCHFV SLEILNLYHN CIRVIPEAIV NLQMLTYLNL
160 170 180 190 200
SRNQLSALPA CLCGLPLKVL IASNNKLGSL PEEIGQLKQL MELDVSCNEI
210 220 230 240 250
TALPQQIGQL KSLRELNVRR NYLKVLPQEL VDLSLVKFDF SCNKVLVIPI
260 270 280 290 300
CFREMKQLQV LLLENNPLQS PPAQICTKGK VHIFKYLSIQ ACQIKTADSL
310 320 330 340 350
YLHTMERPHL HQHVEDGKKD SDSGVGSDNG DKRLSATEPS DEDTVSLNVP
360 370 380 390 400
MSNIMEEEQI IKEDSCHRLS PVKGEFHQEF QPEPSLLGDS TNSGEERDQF
410 420 430 440 450
TDRADGLHSE FMNYKARAED CEELLRIEED VHWQTEGIIS SSKDQDMDIA
460 470 480 490 500
MIEQLREAVD LLQDPNGLST DITERSVLNL YPMGSAEALE LQDSALNGQI
510 520 530 540 550
QLETSPVCEV QSDLTLQSNG SQYSPNEIRE NSPAVSPTTN STAPFGLKPR
560 570 580 590 600
SVFLRPQRNL ESIDPQFTIR RKMEQMREEK ELVEQLRESI EMRLKVSLHE
610 620 630 640 650
DLGAALMDGV VLCHLVNHIR PRSVASIHVP SPAVPKLSMA KCRRNVENFL
660 670 680 690 700
EACRKLGVPE ADLCSPCDIL QLDFRHIRKT VDTLLALGEK APPPTSALRS
710 720
RDLIGFCLVH ILFIVLVYIT YHWNALSA
Length:728
Mass (Da):80,875
Last modified:May 18, 2010 - v3
Checksum:iD4E29414E466DBF8
GO
Isoform 2 (identifier: Q9Y2L9-2) [UniParc]FASTAAdd to basket

Also known as: a, NP81a

The sequence of this isoform differs from the canonical sequence as follows:
     661-696: ADLCSPCDILQLDFRHIRKTVDTLLALGEKAPPPTS → EKLCLPHHILEEKGLVKVGITIQALLDITVTKALFT
     697-728: Missing.

Show »
Length:696
Mass (Da):77,225
Checksum:i696D5FD894F69381
GO
Isoform 3 (identifier: Q9Y2L9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     551-551: S → SDPALILPPISFNTLTQAQTWDSSSYSVPSEGDSDN

Note: No experimental confirmation available.
Show »
Length:763
Mass (Da):84,611
Checksum:i3E357FFC469EB10F
GO

Sequence cautioni

The sequence BAA76860.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence CAH70793.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAH73643.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAI12229.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti326 – 3261G → V in AAI43884 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti234 – 2341S → P.3 Publications
Corresponds to variant rs842381 [ dbSNP | Ensembl ].
VAR_051133
Natural varianti486 – 4861A → S.
Corresponds to variant rs11617392 [ dbSNP | Ensembl ].
VAR_051134

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei551 – 5511S → SDPALILPPISFNTLTQAQT WDSSSYSVPSEGDSDN in isoform 3. 1 PublicationVSP_044474
Alternative sequencei661 – 69636ADLCS…PPPTS → EKLCLPHHILEEKGLVKVGI TIQALLDITVTKALFT in isoform 2. 2 PublicationsVSP_010635Add
BLAST
Alternative sequencei697 – 72832Missing in isoform 2. 2 PublicationsVSP_010636Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY050631 mRNA. Translation: AAK95567.1.
AY050632 mRNA. Translation: AAK95568.1.
AB023233 mRNA. Translation: BAA76860.1. Different initiation.
AL359880, AL136958, AL138704 Genomic DNA. Translation: CAH70793.1. Sequence problems.
AL138704, AL136958, AL359880 Genomic DNA. Translation: CAH73643.1. Sequence problems.
AL136958, AL138704, AL359880 Genomic DNA. Translation: CAI12229.1. Sequence problems.
BC112937 mRNA. Translation: AAI12938.1.
BC117472 mRNA. Translation: AAI17473.1.
BC143883 mRNA. Translation: AAI43884.1.
CCDSiCCDS31972.1. [Q9Y2L9-1]
CCDS53865.1. [Q9Y2L9-3]
CCDS53866.1. [Q9Y2L9-2]
RefSeqiNP_001157683.1. NM_001164211.1.
NP_001157685.1. NM_001164213.1.
NP_055931.1. NM_015116.2.
UniGeneiHs.507971.

Genome annotation databases

EnsembliENST00000311191; ENSP00000308493; ENSG00000136141. [Q9Y2L9-2]
ENST00000389797; ENSP00000374447; ENSG00000136141. [Q9Y2L9-3]
ENST00000389798; ENSP00000374448; ENSG00000136141. [Q9Y2L9-1]
GeneIDi23143.
KEGGihsa:23143.
UCSCiuc001vbj.4. human. [Q9Y2L9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY050631 mRNA. Translation: AAK95567.1.
AY050632 mRNA. Translation: AAK95568.1.
AB023233 mRNA. Translation: BAA76860.1. Different initiation.
AL359880, AL136958, AL138704 Genomic DNA. Translation: CAH70793.1. Sequence problems.
AL138704, AL136958, AL359880 Genomic DNA. Translation: CAH73643.1. Sequence problems.
AL136958, AL138704, AL359880 Genomic DNA. Translation: CAI12229.1. Sequence problems.
BC112937 mRNA. Translation: AAI12938.1.
BC117472 mRNA. Translation: AAI17473.1.
BC143883 mRNA. Translation: AAI43884.1.
CCDSiCCDS31972.1. [Q9Y2L9-1]
CCDS53865.1. [Q9Y2L9-3]
CCDS53866.1. [Q9Y2L9-2]
RefSeqiNP_001157683.1. NM_001164211.1.
NP_001157685.1. NM_001164213.1.
NP_055931.1. NM_015116.2.
UniGeneiHs.507971.

3D structure databases

ProteinModelPortaliQ9Y2L9.
SMRiQ9Y2L9. Positions 63-275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116760. 11 interactions.
IntActiQ9Y2L9. 10 interactions.
STRINGi9606.ENSP00000374447.

PTM databases

iPTMnetiQ9Y2L9.
PhosphoSiteiQ9Y2L9.

Polymorphism and mutation databases

BioMutaiLRCH1.
DMDMi296439310.

Proteomic databases

EPDiQ9Y2L9.
MaxQBiQ9Y2L9.
PaxDbiQ9Y2L9.
PRIDEiQ9Y2L9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000311191; ENSP00000308493; ENSG00000136141. [Q9Y2L9-2]
ENST00000389797; ENSP00000374447; ENSG00000136141. [Q9Y2L9-3]
ENST00000389798; ENSP00000374448; ENSG00000136141. [Q9Y2L9-1]
GeneIDi23143.
KEGGihsa:23143.
UCSCiuc001vbj.4. human. [Q9Y2L9-1]

Organism-specific databases

CTDi23143.
GeneCardsiLRCH1.
HGNCiHGNC:20309. LRCH1.
HPAiHPA021536.
MIMi610368. gene.
neXtProtiNX_Q9Y2L9.
PharmGKBiPA134898200.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0532. Eukaryota.
KOG0619. Eukaryota.
COG4886. LUCA.
GeneTreeiENSGT00840000129676.
HOGENOMiHOG000049055.
HOVERGENiHBG052350.
InParanoidiQ9Y2L9.
OMAiRHIRKTV.
OrthoDBiEOG7288QT.
PhylomeDBiQ9Y2L9.
TreeFamiTF318428.

Miscellaneous databases

ChiTaRSiLRCH1. human.
GenomeRNAii23143.
PROiQ9Y2L9.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y2L9.
CleanExiHS_LRCH1.
ExpressionAtlasiQ9Y2L9. baseline and differential.
GenevisibleiQ9Y2L9. HS.

Family and domain databases

Gene3Di1.10.418.10. 1 hit.
3.80.10.10. 1 hit.
InterProiIPR001715. CH-domain.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
[Graphical view]
PfamiPF00307. CH. 1 hit.
PF13855. LRR_8. 2 hits.
[Graphical view]
SMARTiSM00033. CH. 1 hit.
SM00369. LRR_TYP. 5 hits.
[Graphical view]
SUPFAMiSSF47576. SSF47576. 1 hit.
SSF52058. SSF52058. 1 hit.
PROSITEiPS50021. CH. 1 hit.
PS51450. LRR. 6 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterizing of human NP81 (neuronal protein) gene."
    Guo J.H., Yu L.
    Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT PRO-234.
  2. "Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 6:63-70(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT PRO-234.
    Tissue: Brain.
  3. "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
    Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
    DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION.
  4. "The DNA sequence and analysis of human chromosome 13."
    Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
    Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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] (ISOFORMS 2 AND 3), VARIANT PRO-234.
    Tissue: Brain and Lung.
  6. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-568, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-370, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiLRCH1_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2L9
Secondary accession number(s): B7ZLL5
, F8W6F0, Q17R43, Q2KHR1, Q5TBU9, Q7Z5F6, Q7Z5F7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 22, 2003
Last sequence update: May 18, 2010
Last modified: June 8, 2016
This is version 136 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 13
    Human chromosome 13: 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.