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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctatcggccttttgcagtgttgctccgccttcttggttctttttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG

Basic information

species Vitis vinifera
transcript Vv18s0001g06290.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 2
gtcctatcggccttttgcagtgttgctccgccttcttggttctttttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgt-----agTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG
      | ||    || || |||    |    |   || |   |    ||  |||||  ||  ||   ||  |    || | ||    | || | |||     || || ||||||||||||||||||||||| |||||||||||||| ||||| || || |||
-----gtgggtgcctttcaatgtctaccttgttagctgatgactgaacattagtttgagtttgttctgtaaaattggatatctgatgcctttgtatgtactgcagGCGTGCATTTTTTGACAAGAGGATCTCTCAGGAGGTCAGTGGCGATGCTCTGGGCGAG

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 2
-gtcctatcggccttttgcagtgttgctccgccttcttggttctttttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG
 |  || |     || |       |     |  || |   ||  ||  |       ||   || | |  | | ||  | || ||  | | |  ||||| || |||||||||| ||||||||||||||| ||||| |||||||| ||||| || || || 
agaactgttatagttatctgtccgtttggtgtgttatatatttgttcaagctctcctgttgtaatggtatgt-aattagtgctttcctatcaattgtgcagCCGGGCATTTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 1
gtcctatcggccttttgcagtgttgctccgccttcttggttctttttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG
 || |   |   || |    |||| ||  |    |    || | ||   |  |      | |||||  |    |||||| ||  |     |  | || || || |||||||  |||||||||||||| ||||||||||| |||||||| || || |||
ttcatgaagattttataatttgttcctaagaagccaattttatgttcttttgggcaatgtaatttgtcttgttaaaaatattcctatctttgatttgcagACGAGCATTTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAG

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G24630.1 (Glycine max), 3'ss of exon 2
-gtcctatcggccttttgcagt-gttgctccgccttcttggttctttttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG
 | | | |    |||||    |  ||  |  |     ||  |  || ||| |||  ||   || ||    | | |    ||  |  |   |  | | || |||||||||||||  |||||||||||||| |||||||||  ||| || ||||| || |||
tgacatgttattcttttttttttattaattggaaaattt--tagttgttagtattgttagtttgttaatctgttattgtattctattgttctatatttgcagTCGGGCATTTTGGGACAAGAGGATCTCCCAGGAGGTCCTTGGTGACGCCCTGGGTGAG

upper sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 2
gtcctatcggccttttgcagtgttgctccgccttcttggttctttttaatatgtttgcc--ttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG
     ||     ||      | |    |           || |   |  | | || | |  | | ||  |  |   ||||| ||  |     |  | | ||| || |||||||  |||||||||||||| ||||||||||  |||||||| ||||| |||
--ttcatgaagattaaatgatttgttcctaagaagccaattttacgtgttcttttgggcaatgaattagtcttgttaaaattttcttaactttgatttttagGCGAGCATTTTGGGACAAGAGGATCTCACAGGAGGTCATCGGAGATGCACTCGGTGAG

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|110710093|gb|EE086127.1|EE086127
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110731210|gb|EE109174.1|EE109174
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110369359|gb|EC933517.1|EC933517
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|29782562|gb|CB347995.2|CB347995
EST:     CCGGCCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110724727|gb|EE100810.1|EE100810
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110694354|gb|EE071389.1|EE071389
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110701201|gb|EE078523.1|EE078523
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|30124734|gb|CB910073.1|CB910073
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110422092|gb|EC988404.1|EC988404
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|28962095|gb|CB341128.1|CB341128
EST:     CTTACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: C-GACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110729833|gb|EE106221.1|EE106221
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|71858023|gb|DT007078.1|DT007078
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110698432|gb|EE075922.1|EE075922
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110730616|gb|EE107900.1|EE107900
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
EST: gi|110708627|gb|EE086388.1|EE086388
EST:     CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACT                         TCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT
genomic: CCGACCACAGGATGCCAGAAGAAGCTTGAGATTGACGATGACCAGAAACTgtaagtgctt ... ttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG
 ttttaat  putative branch site (score: 3)
                                   tttgtccacctttt  putative PPT
                      ttatcaaaaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctatcggccttttgcagtgttgctccgccttcttggttctttttaatatgtttgccttatttgcttatcaaaaaatgtttgtccaccttttgtgtagTCGGGCATTTTTTGACAAGAGGATCTCGCAGGAGGTCAGTGGAGATGCCCTCGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - ttttgca
- - - - - - - - - - - - -ctccgcc
- - - - - - - - - - - - - - - - ttcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - gtttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtccacc