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Q8TE12

- LMX1A_HUMAN

UniProt

Q8TE12 - LMX1A_HUMAN

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
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 1 (01 Jun 2002)
      Previous versions | rss
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    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. sequence-specific DNA binding transcription factor activity Source: InterPro
    3. 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. transcription, DNA-templated Source: UniProtKB-KW

    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-SubCell

    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

    ArrayExpressiQ8TE12.
    BgeeiQ8TE12.
    CleanExiHS_LMX1A.
    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.
    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: Q8TE12-1) [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

    MLDGLKMEEN FQSAIDTSAS FSSLLGRAVS PKSVCEGCQR VILDRFLLRL    50
    NDSFWHEQCV QCASCKEPLE TTCFYRDKKL YCKYDYEKLF AVKCGGCFEA 100
    IAPNEFVMRA QKSVYHLSCF CCCVCERQLQ KGDEFVLKEG QLLCKGDYEK 150
    ERELLSLVSP AASDSGKSDD EESLCKSAHG AGKGTAEEGK DHKRPKRPRT 200
    ILTTQQRRAF KASFEVSSKP CRKVRETLAA ETGLSVRVVQ VWFQNQRAKM 250
    KKLARRQQQQ QQDQQNTQRL SSAQTNGGGS AGMEGIMNPY TALPTPQQLL 300
    AIEQSVYSSD PFRQGLTPPQ MPGDHMHPYG AEPLFHDLDS DDTSLSNLGD 350
    CFLATSEAGP LQSRVGNPID HLYSMQNSYF TS 382
    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.
    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

    ArrayExpressi Q8TE12.
    Bgeei Q8TE12.
    CleanExi HS_LMX1A.
    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

    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 1, 2014
    This is version 111 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