Q8RYD9 (TT16_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein TRANSPARENT TESTA 16

Alternative name(s):
Arabidopsis BSISTER MADS-box protein

Gene names

Name:	TT16
Synonyms:	ABS, AGL32
Ordered Locus Names:	At5g23260
ORF Names:	MKD15.12

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	252 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Pathway	Secondary metabolite biosynthesis; flavonoid biosynthesis.
Subcellular location	Nucleus By similarity.
Tissue specificity	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 stage	Expressed during seed development.
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.
Sequence similarities	Contains 1 K-box domain. Contains 1 MADS-box domain.
Sequence caution	The sequence BAB11181.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Flavonoid biosynthesis Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Coiled coil
Ligand	DNA-binding
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	flavonoid biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway ovule development Inferred from mutant phenotype PubMed 16925602. Source: TAIR regulation of cell shape Inferred from mutant phenotype Ref.6. Source: TAIR regulation of double fertilization forming a zygote and endosperm Inferred from genetic interaction PubMed 22176531. Source: TAIR regulation of proanthocyanidin biosynthetic process Inferred from mutant phenotype Ref.6. Source: TAIR seed development Inferred from mutant phenotype PubMed 16925602. Source: TAIR transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding transcription factor activity Inferred from mutant phenotype Ref.6. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SEP1	P29382	3	EBI-621993,EBI-632935
SEP1	Q5XXN7	4	EBI-621993,EBI-621940
SEP3	O22456	7	EBI-621993,EBI-592020

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q8RYD9-1)

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.

Isoform 2 (identifier: Q8RYD9-2)

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

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 252	252	Protein TRANSPARENT TESTA 16		PRO_0000199495
Regions
	Domain	1 – 61	61	MADS-box
	Domain	86 – 176	91	K-box
	Coiled coil	121 – 174	54	Potential
	Compositional bias	180 – 222	43	Gln-rich
Natural variations
	Alternative sequence	142 – 146	5	Missing in isoform 2.		VSP_006257

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: 2C4ECB9D9C1DEEA8	FASTA	252	29,698
	10 20 30 40 50 60 MGRGKIEIKK IENQTARQVT FSKRRTGLIK KTRELSILCD AHIGLIVFSA TGKLSEFCSE 70 80 90 100 110 120 QNRMPQLIDR YLHTNGLRLP DHHDDQEQLH HEMELLRRET CNLELRLRPF HGHDLASIPP 130 140 150 160 170 180 NELDGLERQL EHSVLKVRER KNELMQQQLE NLSRKRRMLE EDNNNMYRWL HEHRAAMEFQ 190 200 210 220 230 240 QAGIDTKPGE YQQFIEQLQC YKPGEYQQFL EQQQQQPNSV LQLATLPSEI DPTYNLQLAQ 250 PNLQNDPTAQ ND
	Isoform 2 [UniParc]. Checksum: 165474BA5A60B555	FASTA	247	29,082
	10 20 30 40 50 60 MGRGKIEIKK IENQTARQVT FSKRRTGLIK KTRELSILCD AHIGLIVFSA TGKLSEFCSE 70 80 90 100 110 120 QNRMPQLIDR YLHTNGLRLP DHHDDQEQLH HEMELLRRET CNLELRLRPF HGHDLASIPP 130 140 150 160 170 180 NELDGLERQL EHSVLKVRER KQQLENLSRK RRMLEEDNNN MYRWLHEHRA AMEFQQAGID 190 200 210 220 230 240 TKPGEYQQFI EQLQCYKPGE YQQFLEQQQQ QPNSVLQLAT LPSEIDPTYN LQLAQPNLQN DPTAQND

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00522403. IPI00535111.
RefSeq	NP_001119264.1. NM_001125792.1. NP_197717.3. NM_122232.3. NP_974823.1. NM_203094.1.
UniGene	At.31019.
3D structure databases
ProteinModelPortal	Q8RYD9.
SMR	Q8RYD9. Positions 2-59.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q8RYD9. 20 interactions.
STRING	3702.AT5G23260.2-P.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT5G23260.2; AT5G23260.2; AT5G23260.
GeneID	832390.
KEGG	ath:AT5G23260.
Organism-specific databases
GeneFarm	3507. 354.
TAIR	At5g23260.
Phylogenomic databases
eggNOG	COG5068.
HOGENOM	HOG000155301.
InParanoid	Q8RYD9.
OMA	IENQTAR.
PhylomeDB	Q8RYD9.
ProtClustDB	CLSN2681063.
Enzyme and pathway databases
UniPathway	UPA00154.
Gene expression databases
ArrayExpress	Q8RYD9.
Genevestigator	Q8RYD9.
GermOnline	AT5G23260. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR002487. TF_Kbox. IPR002100. TF_MADSbox. [Graphical view]
Pfam	PF01486. K-box. 1 hit. PF00319. SRF-TF. 1 hit. [Graphical view]
PRINTS	PR00404. MADSDOMAIN.
SMART	SM00432. MADS. 1 hit. [Graphical view]
SUPFAM	SSF55455. TF_MADSbox. 1 hit.
PROSITE	PS51297. K_BOX. 1 hit. PS00350. MADS_BOX_1. 1 hit. PS50066. MADS_BOX_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

TT16_ARATH

Accession

Primary (citable) accession number: Q8RYD9
Secondary accession number(s): Q540P5, Q9FMX4

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 13, 2002
Last sequence update:	June 1, 2002
Last modified:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program