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Q8RYD9

- TT16_ARATH

UniProt

Q8RYD9 - TT16_ARATH

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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

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. 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
Complete GO annotation...

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-KW
Complete GO annotation...

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

        10         20         30         40         50
MGRGKIEIKK IENQTARQVT FSKRRTGLIK KTRELSILCD AHIGLIVFSA
60 70 80 90 100
TGKLSEFCSE QNRMPQLIDR YLHTNGLRLP DHHDDQEQLH HEMELLRRET
110 120 130 140 150
CNLELRLRPF HGHDLASIPP NELDGLERQL EHSVLKVRER KNELMQQQLE
160 170 180 190 200
NLSRKRRMLE EDNNNMYRWL HEHRAAMEFQ QAGIDTKPGE YQQFIEQLQC
210 220 230 240 250
YKPGEYQQFL EQQQQQPNSV LQLATLPSEI DPTYNLQLAQ PNLQNDPTAQ

ND
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

« Hide 'large scale' publications
  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 29, 2014
This is version 98 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