Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q8RYD9

- TT16_ARATH

UniProt

Q8RYD9 - TT16_ARATH

Protein

Protein TRANSPARENT TESTA 16

Gene

TT16

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 1 (01 Jun 2002)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Transcription factor involved in the developmental regulation of the endothelium and in the accumulation of proanthocyanidins (PAs) or condensed tannins which give the seed its brown pigmentation after oxidation. Necessary for the normal activation of the BANYULS promoter in the endothelium body.

    Pathwayi

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. protein binding Source: IntAct
    3. sequence-specific DNA binding transcription factor activity Source: TAIR

    GO - Biological processi

    1. flavonoid biosynthetic process Source: UniProtKB-UniPathway
    2. ovule development Source: TAIR
    3. regulation of cell shape Source: TAIR
    4. regulation of double fertilization forming a zygote and endosperm Source: TAIR
    5. regulation of proanthocyanidin biosynthetic process Source: TAIR
    6. seed development Source: TAIR
    7. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Biological processi

    Flavonoid biosynthesis, Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    UniPathwayiUPA00154.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein TRANSPARENT TESTA 16
    Alternative name(s):
    Arabidopsis BSISTER MADS-box protein
    Gene namesi
    Name:TT16
    Synonyms:ABS, AGL32
    Ordered Locus Names:At5g23260
    ORF Names:MKD15.12
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G23260.

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 252252Protein TRANSPARENT TESTA 16PRO_0000199495Add
    BLAST

    Proteomic databases

    PRIDEiQ8RYD9.

    Expressioni

    Tissue specificityi

    Expressed in buds, flowers and immature seeds, but not in roots, stems, leaves, seedlings or siliques valves. Expression in seed coat is confined to the endothelium layer.

    Developmental stagei

    Expressed during seed development.

    Gene expression databases

    GenevestigatoriQ8RYD9.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    SEP1P293823EBI-621993,EBI-632935
    SEP1Q5XXN74EBI-621993,EBI-621940
    SEP3O224567EBI-621993,EBI-592020

    Protein-protein interaction databases

    BioGridi17665. 9 interactions.
    IntActiQ8RYD9. 20 interactions.
    STRINGi3702.AT5G23260.2-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8RYD9.
    SMRiQ8RYD9. Positions 2-59.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 6161MADS-boxPROSITE-ProRule annotationAdd
    BLAST
    Domaini86 – 17691K-boxPROSITE-ProRule annotationAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili121 – 17454Sequence AnalysisAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi180 – 22243Gln-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 K-box domain.PROSITE-ProRule annotation
    Contains 1 MADS-box domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiCOG5068.
    HOGENOMiHOG000155301.
    InParanoidiQ8RYD9.
    OMAiIENQTAR.
    PhylomeDBiQ8RYD9.

    Family and domain databases

    InterProiIPR002487. TF_Kbox.
    IPR002100. TF_MADSbox.
    [Graphical view]
    PfamiPF01486. K-box. 1 hit.
    PF00319. SRF-TF. 1 hit.
    [Graphical view]
    PRINTSiPR00404. MADSDOMAIN.
    SMARTiSM00432. MADS. 1 hit.
    [Graphical view]
    SUPFAMiSSF55455. SSF55455. 1 hit.
    PROSITEiPS51297. K_BOX. 1 hit.
    PS00350. MADS_BOX_1. 1 hit.
    PS50066. MADS_BOX_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q8RYD9-1) [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

    MGRGKIEIKK IENQTARQVT FSKRRTGLIK KTRELSILCD AHIGLIVFSA    50
    TGKLSEFCSE QNRMPQLIDR YLHTNGLRLP DHHDDQEQLH HEMELLRRET 100
    CNLELRLRPF HGHDLASIPP NELDGLERQL EHSVLKVRER KNELMQQQLE 150
    NLSRKRRMLE EDNNNMYRWL HEHRAAMEFQ QAGIDTKPGE YQQFIEQLQC 200
    YKPGEYQQFL EQQQQQPNSV LQLATLPSEI DPTYNLQLAQ PNLQNDPTAQ 250
    ND 252
    Length:252
    Mass (Da):29,698
    Last modified:June 1, 2002 - v1
    Checksum:i2C4ECB9D9C1DEEA8
    GO
    Isoform 2 (identifier: Q8RYD9-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         142-146: Missing.

    Show »
    Length:247
    Mass (Da):29,082
    Checksum:i165474BA5A60B555
    GO

    Sequence cautioni

    The sequence BAB11181.1 differs from that shown. Reason: Erroneous gene model prediction.

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei142 – 1465Missing in isoform 2. 2 PublicationsVSP_006257

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ318098 mRNA. Translation: CAC85664.1.
    AY141212 mRNA. Translation: AAN52776.1.
    AB007648 Genomic DNA. Translation: BAB11181.1. Sequence problems.
    CP002688 Genomic DNA. Translation: AED93143.1.
    CP002688 Genomic DNA. Translation: AED93144.1.
    BT030048 mRNA. Translation: ABN04786.1.
    RefSeqiNP_001119264.1. NM_001125792.1.
    NP_197717.3. NM_122232.3. [Q8RYD9-2]
    NP_974823.1. NM_203094.1. [Q8RYD9-1]
    UniGeneiAt.31019.

    Genome annotation databases

    EnsemblPlantsiAT5G23260.2; AT5G23260.2; AT5G23260. [Q8RYD9-1]
    GeneIDi832390.
    KEGGiath:AT5G23260.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ318098 mRNA. Translation: CAC85664.1 .
    AY141212 mRNA. Translation: AAN52776.1 .
    AB007648 Genomic DNA. Translation: BAB11181.1 . Sequence problems.
    CP002688 Genomic DNA. Translation: AED93143.1 .
    CP002688 Genomic DNA. Translation: AED93144.1 .
    BT030048 mRNA. Translation: ABN04786.1 .
    RefSeqi NP_001119264.1. NM_001125792.1.
    NP_197717.3. NM_122232.3. [Q8RYD9-2 ]
    NP_974823.1. NM_203094.1. [Q8RYD9-1 ]
    UniGenei At.31019.

    3D structure databases

    ProteinModelPortali Q8RYD9.
    SMRi Q8RYD9. Positions 2-59.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 17665. 9 interactions.
    IntActi Q8RYD9. 20 interactions.
    STRINGi 3702.AT5G23260.2-P.

    Proteomic databases

    PRIDEi Q8RYD9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G23260.2 ; AT5G23260.2 ; AT5G23260 . [Q8RYD9-1 ]
    GeneIDi 832390.
    KEGGi ath:AT5G23260.

    Organism-specific databases

    GeneFarmi 3507. 354.
    TAIRi AT5G23260.

    Phylogenomic databases

    eggNOGi COG5068.
    HOGENOMi HOG000155301.
    InParanoidi Q8RYD9.
    OMAi IENQTAR.
    PhylomeDBi Q8RYD9.

    Enzyme and pathway databases

    UniPathwayi UPA00154 .

    Gene expression databases

    Genevestigatori Q8RYD9.

    Family and domain databases

    InterProi IPR002487. TF_Kbox.
    IPR002100. TF_MADSbox.
    [Graphical view ]
    Pfami PF01486. K-box. 1 hit.
    PF00319. SRF-TF. 1 hit.
    [Graphical view ]
    PRINTSi PR00404. MADSDOMAIN.
    SMARTi SM00432. MADS. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55455. SSF55455. 1 hit.
    PROSITEi PS51297. K_BOX. 1 hit.
    PS00350. MADS_BOX_1. 1 hit.
    PS50066. MADS_BOX_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A novel MADS-box gene subfamily with sistergroup relationship to class B floral homeotic genes."
      Becker A., Kaufmann K., Freialdenhoven A., Vincent C., Li M.-A., Saedler H., Theissen G.
      Mol. Genet. Genomics 266:942-950(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Strain: cv. Columbia.
      Tissue: Green siliques.
    2. "Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world."
      Parenicova L., de Folter S., Kieffer M., Horner D.S., Favalli C., Busscher J., Cook H.E., Ingram R.M., Kater M.M., Davies B., Angenent G.C., Colombo L.
      Plant Cell 15:1538-1551(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), GENE FAMILY ORGANIZATION.
      Strain: cv. Columbia.
      Tissue: Silique.
    3. "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones."
      Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S.
      DNA Res. 4:401-414(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "Arabidopsis ORF clones."
      Bautista V.R., Kim C.J., Chen H., Wu S.Y., De Los Reyes C., Ecker J.R.
      Submitted (JAN-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Strain: cv. Columbia.
    6. "The TRANSPARENT TESTA16 locus encodes the ARABIDOPSIS BSISTER MADS domain protein and is required for proper development and pigmentation of the seed coat."
      Nesi N., Debeaujon I., Jond C., Stewart A.J., Jenkins G.I., Caboche M., Lepiniec L.
      Plant Cell 14:2463-2479(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, ALTERNATIVE SPLICING.

    Entry informationi

    Entry nameiTT16_ARATH
    AccessioniPrimary (citable) accession number: Q8RYD9
    Secondary accession number(s): Q540P5, Q9FMX4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 13, 2002
    Last sequence update: June 1, 2002
    Last modified: October 1, 2014
    This is version 97 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The two isoforms were always coexpressed in the tissues investigated. The pigmentation of the chalaza-micropyle region is not under the control of ABS, as opposed to the pigmentation of the seed body.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3