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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggggaagtattcctgtaacagctcctgtattatctttttcttcctttactgacattgatcgcatatccaaacatctgttgtttactcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC

Basic information

species Vitis vinifera
transcript Vv02s0025g01410.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 13
gttggggaagtattcctgtaacagctcctgtattatctttttcttcctttactgacattgatcgcatatccaaacatctgttgtttactcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC
             |  || |||        | |||  | || |   |     || ||   |  |||  |  |   |    ||| | |||   | | ||||  |||| | ||  ||  ||||||||| ||||||||||| || || |||||  ||||||| |||||||| ||||| || ||||  |||||||||| ||  ||||| ||||||||||||||||
------------gtggtgaaactttattaattttaattattcccctcccccttgtcacgaacagcaagtgtagcaaa--attgctgact---aatatattcattttgtaac--ttgatcagGTAAAACAAGGTTTAGGGGGTAATGTACGCATTATTTTGTCTGGAGCAGCACCTCTATCTAGACATGTGGAAGGTTTCCTACGGGTGGTGACTTGTGCTC

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 13
gttggggaagtattcctgtaacagctcctgtattatctttttcttcctttactgacattgatcgcatatccaaaca-tctgttgtttactcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC
                                       |||     ||||   |  |  |   |  ||||      | ||        |  || |  ||     ||||   ||||  ||||||||||||||||||||| || |  ||||| |||||||| ||||||||||||||  | ||| | |||||||||| |||  |||| ||||| ||||||||||
--------------------------------------gttttaaaatttataaatttgaactccccatccccttggtatgacaggattttttacta-atcatgattttactacttgatcagGTAAAGCAAGGTTTAGGGGGTAGAGTACGTCTTATTTTGTCTGGAGCCGCACCTTTATCTGCACATGTGGAAGGTTACTTACGGGTGGTTACTTGTGCTC

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 13
gttggggaagtattcctgtaacagctcctgtattatctttttcttcctttactgacattgatcgcatatccaaacatctgttgttt----actcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC
                                       |||     ||||   |  |||| |   |  |||  |   || | |      | |  |     ||     ||||   ||||  ||||||||||||||||||||| || |  ||||| |||||||| |||||||| |||||  | ||| | |||||||||| |||  |||| ||||||||||||||||
--------------------------------------gttttaaaatttataaaatttgaac---ttcccagccccttggtatgacaggattttttactaatcacaattttactacttgatcagGTAAAGCAAGGTTTAGGGGGTAGAGTACGTCTTATTTTGTCTGGAGCAGCACCTTTATCTGCACATGTGGAAGGTTACTTACGGGTGGTGACTTGTGCTC

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G02620.1 (Glycine max), 3'ss of exon 13
gttggggaagtattcctgtaacagctcctgtattatctttttcttcctttactgacattgatcgcatatccaaacatctgttgtttactcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGG-AAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC---------------
             |  || |||  |     | |||  | || |   ||    ||  |   |  |||  |  |   |    ||| | |||   | | ||||   ||||||  ||||  ||||||||||||||||||||| || ||| |||||  | ||||| |||||||| ||||| || ||||  || ||||||| ||  ||||||||||||||||||||||               
------------gtggtgaaacttcattaattttaattattcccctctgccttgttaggaacagcaagtgtagcgaa--attgctgact---aatatatt--ctttttgtaacttgatcaggtaaagcaaggtttagGGGGGAAATGTACGTATAATTTTGTCTGGAGCAGCACCTCTATCTAGACACGTGGAAGGTTTCCTACGAGTGGTGACTTGTGCTCTCATATCCTTCAATG

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|349816864|gb|FQ399732.1|FQ399732
EST:     TTAAAACCCTAGAGGCAGCTCCTATTTGTGATAAAATAGTCTTTGGCAAG                         GTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCA
genomic: TTAAAACCCTAGAGGCAGCTCCTATTTGTGATAAAATAGTCTTTGGCAAGgttggggaag ... acttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCA
EST: gi|351053855|gb|FQ441621.1|FQ441621
EST:     TTAAAACCCTAGAGGCAGCTCCTATTTGTGATAAAATAGTCTTTGGCAAG                         GTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCA
genomic: TTAAAACCCTAGAGGCAGCTCCTATTTGTGATAAAATAGTCTTTGGCAAGgttggggaag ... acttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCA
EST: gi|351028751|gb|FQ433181.1|FQ433181
EST:     TGAGCTTTGGCAAGGTTACACCTGAACAAAGGGAAGAAGTTGAAAAGTTTGGTTTGGCCATATATTCTTGGGAGGAATTCTTGCAACTG
genomic: TGAGCTTTGGCAAGGTTACACCTGAACAAAGGGAAGAAGTTGAAAAGTTTGGTTTGGCCATATATTATTGGGAGGAATTCTTGCAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccaaacatctgttgtttactcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC
                                      ttttgac  putative branch site (score: 3)
                                            cacttcctc  CT-rich tract
                                    ttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggggaagtattcctgtaacagctcctgtattatctttttcttcctttactgacattgatcgcatatccaaacatctgttgtttactcctagtgtattggttttttgacacttcctcagGTAAAGCAAGGTTTAGGTGGAAACGTACGACTTATTTTATCTGGAGCCGCACCACTCTCTACCCATGTGGAAGCTTATCTACGAGTGGTGACTTGTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG