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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcattttctagcaaaataaacacacctacaatttccacatttccccctcccttttcctcttgtatccagtgtaatggaaatattaaatctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGAT

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G17110.1 (Glycine max), 3'ss of exon 1
tttcattttctagcaaaataaacacacctacaatttccacatttccccctcccttttcctcttgtatccagtgtaatggaaatattaaatctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGAT
 | |    || | ||         |   | ||    |||  ||||  |||   | ||  ||   |  |   | ||||     | || | || |||||||||| |||||||| |||||||||||||| || || |||||||| ||||| |||||  | || ||||||
gtaccccctccaccactcctttttctttt-catcccccaagtttcaacctttttatttatca-atgccttttttaat-----tcttcattcattcctcagGTCACTGTTTATCAATGTCTTGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71864778|gb|DT013833.1|DT013833
EST:     TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|161719190|gb|FC065436.1|FC065436
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|351053554|gb|FQ459301.1|FQ459301
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|351036699|gb|FQ457412.1|FQ457412
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|351043856|gb|FQ452650.1|FQ452650
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|352791431|gb|FQ481010.1|FQ481010
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|161711022|gb|FC059448.1|FC059448
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|294965480|gb|GW839051.1|GW839051
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     TCATCGACTCTCGCTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGA                         GTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAATCT
genomic: TCATCGACTCTCGTTACTTCAATGTCTTCGCTACTGTCGGCGGCAATCGAgtacttctcc ... ctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctcccttttcctcttgtatccagtgtaatggaaatattaaatctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGAT
                                            tctttcctc  CT-rich tract
                            taatggaaatattaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcattttctagcaaaataaacacacctacaatttccacatttccccctcccttttcctcttgtatccagtgtaatggaaatattaaatctttcctcagGTAACTGTTTACCAATGTCTTGAAGGGGGCGTCATTGCTGTCTTGCAGTCTTACATTGATGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - aaaataa
- - - - - - - - - - -acacacc
- - - - - - - - - - - - - - - - - ttccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaata