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Protein

LIM/homeobox protein Lhx9

Gene

LHX9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in gonadal development.By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi267 – 32660HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM/homeobox protein Lhx9
Short name:
LIM homeobox protein 9
Gene namesi
Name:LHX9
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:14222. LHX9.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA30368.

Polymorphism and mutation databases

BioMutaiLHX9.
DMDMi224471883.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 397397LIM/homeobox protein Lhx9PRO_0000075798Add
BLAST

Proteomic databases

EPDiQ9NQ69.
PaxDbiQ9NQ69.
PRIDEiQ9NQ69.

PTM databases

PhosphoSiteiQ9NQ69.

Expressioni

Gene expression databases

BgeeiQ9NQ69.
CleanExiHS_LHX9.
ExpressionAtlasiQ9NQ69. baseline and differential.
GenevisibleiQ9NQ69. HS.

Organism-specific databases

HPAiHPA009695.

Interactioni

Subunit structurei

Interacts with LDB1 and LDB2.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
A8KAD63EBI-10175218,EBI-10174974
KHKP500533EBI-10175218,EBI-1053974

Protein-protein interaction databases

BioGridi121280. 8 interactions.
IntActiQ9NQ69. 2 interactions.
STRINGi9606.ENSP00000356357.

Structurei

Secondary structure

1
397
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi276 – 28813Combined sources
Helixi294 – 30310Combined sources
Helixi308 – 32720Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DMQNMR-A268-334[»]
ProteinModelPortaliQ9NQ69.
SMRiQ9NQ69. Positions 71-193, 268-334.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NQ69.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini69 – 13062LIM zinc-binding 1PROSITE-ProRule annotationAdd
BLAST
Domaini131 – 19363LIM zinc-binding 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
Contains 2 LIM zinc-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox, LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG0490. Eukaryota.
ENOG410YIJ3. LUCA.
GeneTreeiENSGT00760000118921.
HOVERGENiHBG006262.
InParanoidiQ9NQ69.
KOiK09373.
OMAiILGHYSH.
OrthoDBiEOG7966GV.
PhylomeDBiQ9NQ69.
TreeFamiTF315442.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NQ69-1) [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
MEIVGCRAED NSCPFRPPAM LFHGISGGHI QGIMEEMERR SKTEARLAKG
60 70 80 90 100
AQLNGRDAGM PPLSPEKPAL CAGCGGKISD RYYLLAVDKQ WHLRCLKCCE
110 120 130 140 150
CKLALESELT CFAKDGSIYC KEDYYRRFSV QRCARCHLGI SASEMVMRAR
160 170 180 190 200
DSVYHLSCFT CSTCNKTLTT GDHFGMKDSL VYCRAHFETL LQGEYPPQLS
210 220 230 240 250
YTELAAKSGG LALPYFNGTG TVQKGRPRKR KSPALGVDIV NYNSGCNENE
260 270 280 290 300
ADHLDRDQQP YPPSQKTKRM RTSFKHHQLR TMKSYFAINH NPDAKDLKQL
310 320 330 340 350
AQKTGLTKRV LQVWFQNARA KFRRNLLRQE NGGVDKADGT SLPAPPSADS
360 370 380 390
GALTPPGTAT TLTDLTNPTI TVVTSVTSNM DSHESGSPSQ TTLTNLF
Length:397
Mass (Da):43,976
Last modified:March 3, 2009 - v3
Checksum:iFA8BBB550A5FCE03
GO
Isoform 2 (identifier: Q9NQ69-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-18: MEIVGCRAEDNSCPFRPP → MLNGTTLEA

Show »
Length:388
Mass (Da):42,904
Checksum:iA4DC8B914D7C3B66
GO
Isoform 3 (identifier: Q9NQ69-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-18: MEIVGCRAEDNSCPFRPP → MLNGTTLEA
     313-397: VWFQNARAKF...PSQTTLTNLF → GEQILGHYSQTSRRLKIP

Show »
Length:321
Mass (Da):36,056
Checksum:iD26CE988920D6DC3
GO
Isoform 4 (identifier: Q9NQ69-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     313-397: VWFQNARAKF...PSQTTLTNLF → GEQILGHYSQTSRRLKIP

Show »
Length:330
Mass (Da):37,129
Checksum:i4A819459D3BB038B
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 1818MEIVG…PFRPP → MLNGTTLEA in isoform 2 and isoform 3. 1 PublicationVSP_036428Add
BLAST
Alternative sequencei313 – 39785VWFQN…LTNLF → GEQILGHYSQTSRRLKIP in isoform 3 and isoform 4. CuratedVSP_036429Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ277915 mRNA. Translation: CAB97493.1.
AJ277916
, AJ277917, AJ277918, AJ277919, AJ277920 Genomic DNA. Translation: CAB98128.1. Sequence problems.
AJ296272 mRNA. Translation: CAC33174.1.
AY273889 mRNA. Translation: AAP32471.2.
AL590115 Genomic DNA. Translation: CAH71760.1.
AL590115 Genomic DNA. Translation: CAH71761.1.
AL590115 Genomic DNA. Translation: CAH71763.1.
AL590115 Genomic DNA. Translation: CAH71764.1.
CH471067 Genomic DNA. Translation: EAW91290.1.
CH471067 Genomic DNA. Translation: EAW91292.1.
BC131622 mRNA. Translation: AAI31623.1.
CCDSiCCDS1393.1. [Q9NQ69-1]
CCDS30962.1. [Q9NQ69-2]
RefSeqiNP_001014434.1. NM_001014434.1. [Q9NQ69-2]
NP_064589.2. NM_020204.2. [Q9NQ69-1]
XP_005245407.1. XM_005245350.2. [Q9NQ69-4]
UniGeneiHs.442578.
Hs.706475.

Genome annotation databases

EnsembliENST00000367387; ENSP00000356357; ENSG00000143355. [Q9NQ69-1]
ENST00000367390; ENSP00000356360; ENSG00000143355. [Q9NQ69-2]
ENST00000367391; ENSP00000356361; ENSG00000143355. [Q9NQ69-3]
GeneIDi56956.
KEGGihsa:56956.
UCSCiuc001gui.2. human. [Q9NQ69-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ277915 mRNA. Translation: CAB97493.1.
AJ277916
, AJ277917, AJ277918, AJ277919, AJ277920 Genomic DNA. Translation: CAB98128.1. Sequence problems.
AJ296272 mRNA. Translation: CAC33174.1.
AY273889 mRNA. Translation: AAP32471.2.
AL590115 Genomic DNA. Translation: CAH71760.1.
AL590115 Genomic DNA. Translation: CAH71761.1.
AL590115 Genomic DNA. Translation: CAH71763.1.
AL590115 Genomic DNA. Translation: CAH71764.1.
CH471067 Genomic DNA. Translation: EAW91290.1.
CH471067 Genomic DNA. Translation: EAW91292.1.
BC131622 mRNA. Translation: AAI31623.1.
CCDSiCCDS1393.1. [Q9NQ69-1]
CCDS30962.1. [Q9NQ69-2]
RefSeqiNP_001014434.1. NM_001014434.1. [Q9NQ69-2]
NP_064589.2. NM_020204.2. [Q9NQ69-1]
XP_005245407.1. XM_005245350.2. [Q9NQ69-4]
UniGeneiHs.442578.
Hs.706475.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DMQNMR-A268-334[»]
ProteinModelPortaliQ9NQ69.
SMRiQ9NQ69. Positions 71-193, 268-334.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121280. 8 interactions.
IntActiQ9NQ69. 2 interactions.
STRINGi9606.ENSP00000356357.

PTM databases

PhosphoSiteiQ9NQ69.

Polymorphism and mutation databases

BioMutaiLHX9.
DMDMi224471883.

Proteomic databases

EPDiQ9NQ69.
PaxDbiQ9NQ69.
PRIDEiQ9NQ69.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000367387; ENSP00000356357; ENSG00000143355. [Q9NQ69-1]
ENST00000367390; ENSP00000356360; ENSG00000143355. [Q9NQ69-2]
ENST00000367391; ENSP00000356361; ENSG00000143355. [Q9NQ69-3]
GeneIDi56956.
KEGGihsa:56956.
UCSCiuc001gui.2. human. [Q9NQ69-1]

Organism-specific databases

CTDi56956.
GeneCardsiLHX9.
HGNCiHGNC:14222. LHX9.
HPAiHPA009695.
MIMi606066. gene.
neXtProtiNX_Q9NQ69.
PharmGKBiPA30368.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0490. Eukaryota.
ENOG410YIJ3. LUCA.
GeneTreeiENSGT00760000118921.
HOVERGENiHBG006262.
InParanoidiQ9NQ69.
KOiK09373.
OMAiILGHYSH.
OrthoDBiEOG7966GV.
PhylomeDBiQ9NQ69.
TreeFamiTF315442.

Miscellaneous databases

EvolutionaryTraceiQ9NQ69.
GenomeRNAii56956.
NextBioi62575.
PROiQ9NQ69.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NQ69.
CleanExiHS_LHX9.
ExpressionAtlasiQ9NQ69. baseline and differential.
GenevisibleiQ9NQ69. HS.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view]
SMARTiSM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Absence of mutations involving the LIM homeobox domain gene LHX9 in 46,XY gonadal agenesis and dysgenesis."
    Ottolenghi C., Moreira-Filho C., Mendonca B.B., Barbieri M., Fellous M., Berkovitz G.D., McElreavey K.
    J. Clin. Endocrinol. Metab. 86:2465-2469(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 2).
    Tissue: Testis.
  2. "Cloning and characterization of human novel LIM-homeobox 9 gene."
    Shan Y.X., Pan J., Guo Z.K., Geng D.C., Huang C.Q., Yu L.
    Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. 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] (ISOFORM 1).
  6. "Solution structure of the homeobox domain of LIM/homeobox protein LHX9."
    RIKEN structural genomics initiative (RSGI)
    Submitted (OCT-2006) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 268-334.

Entry informationi

Entry nameiLHX9_HUMAN
AccessioniPrimary (citable) accession number: Q9NQ69
Secondary accession number(s): Q5VUE2
, Q5VUE3, Q5VUE6, Q86UH2, Q9BYU6, Q9NQ70
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2001
Last sequence update: March 3, 2009
Last modified: March 16, 2016
This is version 131 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.