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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattacgtaataagaacgaagataatctctcttgaaattctttttgagcagagaactgaacatgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG

Basic information

species Vitis vinifera
transcript Vv04s0023g03040.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G37360.1 (Glycine max), 3'ss of exon 2
------gtaagtattacg-taataagaacgaaga-taatctc--------tcttgaaattctttttgagcagagaactgaacatgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG---
        || ||  | | ||| || |   ||   || | ||        |  | ||||  |   |  |   |  || | | |||  ||   | ||  |||||||||||||| | | |||| ||||||||| || |||| | |||||||||||| || ||||| ||||||||||| |  |     | | ||||||| ||||   
gtttattgaattagcatggtaacaaaactaaattctagtttcagtagcactaattaaatgttcactcggatcatgaccgca-atgctatgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTGGAAGAGAGGGGGATGAGGTATGTCACAGCTGTGGTGGAGGAAGGAGG---AATCCAGGTGGACCAGGTGT

upper sequence: Vv04s0023g03040.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G07940.1 (Glycine max), 3'ss of exon 2
------gtaagtattacgtaataagaacgaag---------ataatctctcttgaaattctttt-tgagcagagaactgaac-atgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG---
       |||| ||   |||| || |   ||          |  ||| ||  ||||||  |     |      ||  |   | |||   |   | ||  |||||||||||||| | | |||| ||||||||| |  |||| | |||||||||||| |||||||| ||||||||||| |  |     | | ||||||| ||||   
tattgaataagcatg--gtaacaaaagttaaatctagtttcagcatcactaatgaaatgttcacacggatcatgacttatgcgatgctttgattttgggcagTGTACTGATGTTGAACTTGTTAAGAAGAGGTTAGAAGAGAGGGGGATGAGGTATGTGACAGCTGTGGTGGAGGAAGGAGG---AATCCAGGTGGACCAGGTGT
















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|161720994|gb|FC070361.1|FC070361
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|30300641|gb|CB977435.1|CB977435
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|77587531|gb|DV222931.1|DV222931
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|349824516|gb|FQ413183.1|FQ413183
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|32247559|gb|CD713378.1|CD713378
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|110689897|gb|EE066521.1|EE066521
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|30251894|gb|CB969627.1|CB969627
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|110693894|gb|EE070523.1|EE070523
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|351054863|gb|FQ462893.1|FQ462893
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|351024125|gb|FQ423548.1|FQ423548
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|110732323|gb|EE107507.1|EE107507
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|110397382|gb|EC963117.1|EC963117
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|110700259|gb|EE078095.1|EE078095
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|30255833|gb|CB971965.1|CB971965
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|32269228|gb|CD718387.1|CD718387
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|77586048|gb|DV222123.1|DV222123
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|161720466|gb|FC070578.1|FC070578
EST:     TCAATGATCCTCGACCCATTAATCCCAACGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|349824424|gb|FQ417811.1|FQ417811
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|71876055|gb|DT025110.1|DT025110
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|30251887|gb|CB969620.1|CB969620
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|349811351|gb|FQ407577.1|FQ407577
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
EST: gi|161706558|gb|FC055847.1|FC055847
EST:     TCAATGATCCTCGACCCATTAATCCCTAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTG
EST: gi|110731806|gb|EE106541.1|EE106541
EST:     TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTG                         TGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG
genomic: TCAATGATCCTCGACCCATTAATCCCAAGGATAACCACATCTCCTTCTTGgtaagtatta ... ctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcttgaaattctttttgagcagagaactgaacatgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG
      ttgaaattcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattacgtaataagaacgaagataatctctcttgaaattctttttgagcagagaactgaacatgggattgctgtgaacagTGTACTGATGTGGGAATTGTGAAGAAGAGGCTGCAAGAAATGGGGATGAGGTACGTGACAGCAGTGGTGGAGGACGACGATGCGAACAAGGTGGATCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA