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Q8TE12

- LMX1A_HUMAN

UniProt

Q8TE12 - LMX1A_HUMAN

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Protein

LIM homeobox transcription factor 1-alpha

Gene

LMX1A

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

Functioni

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi195 – 25460HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. sequence-specific DNA binding Source: InterPro
  2. zinc ion binding Source: InterPro

GO - Biological processi

  1. axon guidance Source: Ensembl
  2. central nervous system neuron differentiation Source: Ensembl
  3. cerebellum development Source: Ensembl
  4. dentate gyrus development Source: Ensembl
  5. dopaminergic neuron differentiation Source: Ensembl
  6. midbrain development Source: Ensembl
  7. negative regulation of neuron differentiation Source: Ensembl
  8. regulation of cell growth Source: Ensembl
  9. regulation of transcription, DNA-templated Source: UniProtKB-KW
  10. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM homeobox transcription factor 1-alpha
Alternative name(s):
LIM/homeobox protein 1.1
Short name:
LMX-1.1
LIM/homeobox protein LMX1A
Gene namesi
Name:LMX1A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:6653. LMX1A.

Subcellular locationi

Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA30416.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 382382LIM homeobox transcription factor 1-alphaPRO_0000075825Add
BLAST

Proteomic databases

PaxDbiQ8TE12.
PRIDEiQ8TE12.

PTM databases

PhosphoSiteiQ8TE12.

Expressioni

Tissue specificityi

Isoform 1 is expressed in many tissues. Not found in heart, liver, spleen and testis. Relatively highly expressed in fetal brain. Isoform LMX1A-4B is expressed in testis.1 Publication

Gene expression databases

BgeeiQ8TE12.
CleanExiHS_LMX1A.
ExpressionAtlasiQ8TE12. baseline.
GenevestigatoriQ8TE12.

Organism-specific databases

HPAiHPA028051.
HPA030088.

Interactioni

Protein-protein interaction databases

BioGridi110194. 5 interactions.
STRINGi9606.ENSP00000294816.

Structurei

3D structure databases

ProteinModelPortaliQ8TE12.
SMRiQ8TE12. Positions 34-153, 196-258.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini33 – 9260LIM zinc-binding 1PROSITE-ProRule annotationAdd
BLAST
Domaini92 – 15463LIM zinc-binding 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi240 – 27435Gln-richAdd
BLAST
Compositional biasi257 – 2659Poly-Gln

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

eggNOGiNOG243427.
GeneTreeiENSGT00760000118921.
HOGENOMiHOG000231629.
HOVERGENiHBG052335.
InParanoidiQ8TE12.
KOiK09371.
OMAiYNSDPFR.
OrthoDBiEOG7BZVTB.
PhylomeDBiQ8TE12.
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 (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q8TE12) [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
MLDGLKMEEN FQSAIDTSAS FSSLLGRAVS PKSVCEGCQR VILDRFLLRL
60 70 80 90 100
NDSFWHEQCV QCASCKEPLE TTCFYRDKKL YCKYDYEKLF AVKCGGCFEA
110 120 130 140 150
IAPNEFVMRA QKSVYHLSCF CCCVCERQLQ KGDEFVLKEG QLLCKGDYEK
160 170 180 190 200
ERELLSLVSP AASDSGKSDD EESLCKSAHG AGKGTAEEGK DHKRPKRPRT
210 220 230 240 250
ILTTQQRRAF KASFEVSSKP CRKVRETLAA ETGLSVRVVQ VWFQNQRAKM
260 270 280 290 300
KKLARRQQQQ QQDQQNTQRL SSAQTNGGGS AGMEGIMNPY TALPTPQQLL
310 320 330 340 350
AIEQSVYSSD PFRQGLTPPQ MPGDHMHPYG AEPLFHDLDS DDTSLSNLGD
360 370 380
CFLATSEAGP LQSRVGNPID HLYSMQNSYF TS
Length:382
Mass (Da):42,747
Last modified:June 1, 2002 - v1
Checksum:i55424762757FF5FD
GO
Isoform LMX1A-4AB (identifier: Q8TE12-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-249: Missing.

Show »
Length:133
Mass (Da):14,615
Checksum:iD58B4EF35A69D5F1
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 249249Missing in isoform LMX1A-4AB. 1 PublicationVSP_003112Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY078398
, AY078391, AY078392, AY078393, AY078394, AY078395, AY078396, AY078397 Genomic DNA. Translation: AAL82892.1.
AY078398, AY078396, AY078397 Genomic DNA. Translation: AAL82893.1.
AK127724 mRNA. Translation: BAG54558.1.
AL390730, AL160058 Genomic DNA. Translation: CAH73258.1.
AL160058, AL390730 Genomic DNA. Translation: CAH71967.1.
CH471067 Genomic DNA. Translation: EAW90744.1.
BC119743 mRNA. Translation: AAI19744.1.
BC119744 mRNA. Translation: AAI19745.1.
CCDSiCCDS1247.1. [Q8TE12-1]
RefSeqiNP_001167540.1. NM_001174069.1. [Q8TE12-1]
NP_796372.1. NM_177398.3. [Q8TE12-1]
UniGeneiHs.667312.

Genome annotation databases

EnsembliENST00000294816; ENSP00000294816; ENSG00000162761. [Q8TE12-1]
ENST00000342310; ENSP00000340226; ENSG00000162761. [Q8TE12-1]
ENST00000367893; ENSP00000356868; ENSG00000162761. [Q8TE12-1]
GeneIDi4009.
KEGGihsa:4009.
UCSCiuc001gcz.2. human. [Q8TE12-1]
uc021pdy.1. human. [Q8TE12-2]

Polymorphism databases

DMDMi27923801.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AY078398
, AY078391 , AY078392 , AY078393 , AY078394 , AY078395 , AY078396 , AY078397 Genomic DNA. Translation: AAL82892.1 .
AY078398 , AY078396 , AY078397 Genomic DNA. Translation: AAL82893.1 .
AK127724 mRNA. Translation: BAG54558.1 .
AL390730 , AL160058 Genomic DNA. Translation: CAH73258.1 .
AL160058 , AL390730 Genomic DNA. Translation: CAH71967.1 .
CH471067 Genomic DNA. Translation: EAW90744.1 .
BC119743 mRNA. Translation: AAI19744.1 .
BC119744 mRNA. Translation: AAI19745.1 .
CCDSi CCDS1247.1. [Q8TE12-1 ]
RefSeqi NP_001167540.1. NM_001174069.1. [Q8TE12-1 ]
NP_796372.1. NM_177398.3. [Q8TE12-1 ]
UniGenei Hs.667312.

3D structure databases

ProteinModelPortali Q8TE12.
SMRi Q8TE12. Positions 34-153, 196-258.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 110194. 5 interactions.
STRINGi 9606.ENSP00000294816.

PTM databases

PhosphoSitei Q8TE12.

Polymorphism databases

DMDMi 27923801.

Proteomic databases

PaxDbi Q8TE12.
PRIDEi Q8TE12.

Protocols and materials databases

DNASUi 4009.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000294816 ; ENSP00000294816 ; ENSG00000162761 . [Q8TE12-1 ]
ENST00000342310 ; ENSP00000340226 ; ENSG00000162761 . [Q8TE12-1 ]
ENST00000367893 ; ENSP00000356868 ; ENSG00000162761 . [Q8TE12-1 ]
GeneIDi 4009.
KEGGi hsa:4009.
UCSCi uc001gcz.2. human. [Q8TE12-1 ]
uc021pdy.1. human. [Q8TE12-2 ]

Organism-specific databases

CTDi 4009.
GeneCardsi GC01M165171.
HGNCi HGNC:6653. LMX1A.
HPAi HPA028051.
HPA030088.
MIMi 600298. gene.
neXtProti NX_Q8TE12.
PharmGKBi PA30416.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG243427.
GeneTreei ENSGT00760000118921.
HOGENOMi HOG000231629.
HOVERGENi HBG052335.
InParanoidi Q8TE12.
KOi K09371.
OMAi YNSDPFR.
OrthoDBi EOG7BZVTB.
PhylomeDBi Q8TE12.
TreeFami TF315442.

Miscellaneous databases

GeneWikii LMX1A.
GenomeRNAii 4009.
NextBioi 15724.
PROi Q8TE12.
SOURCEi Search...

Gene expression databases

Bgeei Q8TE12.
CleanExi HS_LMX1A.
ExpressionAtlasi Q8TE12. baseline.
Genevestigatori Q8TE12.

Family and domain databases

Gene3Di 1.10.10.60. 1 hit.
2.10.110.10. 2 hits.
InterProi IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001781. Znf_LIM.
[Graphical view ]
Pfami PF00046. Homeobox. 1 hit.
PF00412. LIM. 2 hits.
[Graphical view ]
SMARTi SM00389. HOX. 1 hit.
SM00132. LIM. 2 hits.
[Graphical view ]
SUPFAMi SSF46689. SSF46689. 1 hit.
PROSITEi PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, expression and genomic structure of human LMX1A, and variant screening in Pima Indians."
    Thameem F., Wolford J.K., Wang J., German M.S., Bogardus C., Prochazka M.
    Gene 290:217-225(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, TISSUE SPECIFICITY.
  2. "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 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 LMX1A-4AB).

Entry informationi

Entry nameiLMX1A_HUMAN
AccessioniPrimary (citable) accession number: Q8TE12
Secondary accession number(s): B3KXP6
, Q0VDB5, Q5VWG4, Q8TE11
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 27, 2003
Last sequence update: June 1, 2002
Last modified: October 29, 2014
This is version 112 of the entry and version 1 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 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3