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Table 1 CArG-box sequences found in the promoters of ripening-induced genes.

From: Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

Site

CArG-box and its flanking sequences (5' to 3')1)

Motif 2)

CArG-box position (bps)3)

ACS2-a4)

AGCTATT- CTAAAAAAAG -TATCACATA5)

Possible

X59139 (1,365 - 1,374) (+)

ACS2-b

AAATGCAC- CCTAAATTAG -TCAAATAT5)

Possible

X59139 (2,654 - 2,663) (+)

ACS4-a

ATCAAACA- CAAATATAAG -TTTGGAAC5)

Atypical

M88487 (567 - 576) (+)

ACS4-b

ATTAAACA- CAATTTTAAG -AAACTTTT5)

Atypical

M88487 (1,201 - 1,210) (+)

ACS4-c

TGAAATAT- CTAGTTAAAG -ATATGTAC5)

Atypical

M88487 (1,802 - 1,811) (+)

ACO1

GGTTGAAT- CTATAAAAAG -AAAAATAT

Possible

X58273 (1,285 - 1,294) (+)

ETR3-a

GGAGAAAT- CCTATAATAG -GGCAAACA

Intermediate

AY600437 (3,121 - 3,130) (+)

 

GAGAAATC- CTATAATAGG -GCAAACAC

Possible

AY600437 (3,122 - 3,131) (+)

 

GGCAAACA- CCAAAAATAG -CTTGGAGT

Intermediate

AY600437 (3,139 - 3,148) (+)

ETR3-b

AAATTTCA- CTTAATATGG -ACTAGAGA

Possible

AY600437 (3,745 - 3,754) (+)

PG-a

GCACCAAT- CTAATTTAGG -TTGAGCCG

Possible

scaffold01076 (1,534,540 - 1,534,549) (-)

PG-b

CTTAAAAT- CTATAAATAG -ACAAACCC

MEF2-like

scaffold01076 (1,533,632 - 1,533,641) (-)

TBG4-a

TATATGCT- CTATTTTTGG -ACGGCAGG5)

Possible

scaffold00061 (457,025 - 457,034) (+)

TBG4-b

TTTGGGCC- CCATTTAAGG -GATTGGGC5)

SRF-like

scaffold00061 (457,311 - 457,320) (+)

EXP1-a

TTATTTTA- CATTTATATG -TTATTATT

Atypical

scaffold00114 (3,118,161 - 3,118,170) (-)

EXP1-b

TGATGCTT- CAATTTAAAG -AAAATAAA5)

Atypical

scaffold00114 (3,117,729 - 3,117,738) (-)

MAN4

TTTCTTTT- CCATTTATAG -AAAAACCA5)

Intermediate

scaffold01157 (9,316,653 - 9,316,662) (-)

PSY1

TATGTGTA- CCAAAATTAG -AAAATCAG

Intermediate

scaffold00066 (364,464 - 364,473) (+)

 

CTTGTTGA- CTAAATATAG -AATGCATC

MEF2-like

scaffold00066 (364,504 - 364,513) (+)

INV

TTATGATA- CTTAATATGG -TAATCTTT

Possible

Z12027 (1,634 - 1,643) (+)

 

TTCTCACT- CTATAAATAG -AGTTGTTC

MEF2-like

Z12027 (1,667 - 1,676) (+)

RIN-a

GTTGCACT- CTAAAAAAAG -TTAAAAGG5)

Possible

scaffold00243 (210,835 - 210,844) (-)

RIN-b

ACAAAGAA- CCATTAAAAG -GTTAAAAA5)

Intermediate

scaffold00243 (210,262 - 210,271) (-)

  1. 1) CArG-box sequences are underlined.
  2. 2) CArG-box sequences in the exhibited strand were grouped into motifs. Groups of the motif sequences are referenced in the text.
  3. 3) Scaffolds followed by Arabic numerals indicate that the sequences originate from WGS data. Symbols + and - in parentheses indicate that the CArG boxes displayed are presented in either the exhibited (+) or complementary (-) strands.
  4. 4) Site was previously described [6].
  5. 5) Sequences were used for in vitro gel retardation assays.