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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatcttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG

Basic information

species Vitis vinifera
transcript Vv04s0023g03820.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G36890.1 (Glycine max), 3'ss of exon 5
--ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatc-ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
   ||   | |     ||         ||    | |    || |  ||  ||   ||    | |     | |   | |||  ||  |    |  ||  || |||||||||||||||||||||| |||||||||||||| |||||||| |||||||||||||||| |
ctgtgacatcaaactattcccaaaaaaatt-gtttctgcattctccttttcagtaaattttcctctctgattttaactct--ttcccgtggcacttattttagGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 5
-ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatc-ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
  ||   | |     ||       | |     | |    || |  ||  |    ||    | |     | |   | |||  ||  |    |  ||  || ||||||||||||||||||| || |||||||||||||| |||||||| |||||||||||||||| |
tgtgacatcaaactattcccaaaataaattgtttctggattctccttttccgtaaattttcctctcttattattactct--ttcccgtggcacttattttagGCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G08350.2 (Glycine max), 3'ss of exon 5
ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatc-ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
     |  |     |   |    | |     | |    || |  ||  |    ||    | |     | |   | |||  ||  |    |  ||  || ||||||||||||||||||| || |||||||||||||| |||||||| |||||||||||||||| |
-----tcaaactattcccaaa-ataaattgtttctggattctccttttccgtaaattttcctctcttattattactct--ttcccgtggcacttattttaggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatcttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
      | || ||    |  | ||      | |   | || | ||         | || ||       ||| |         ||||| |  ||| | ||||| |||||||||||  ||||||||||  ||||||||||||||||||||||||||||||||| |
-----gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactc------atcac-------ccatcacttaattt-tgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG

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|110715477|gb|EE093574.1|EE093574
EST:     AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71879469|gb|DT028524.1|DT028524
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|352785790|gb|FQ475793.1|FQ475793
EST:     AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71878029|gb|DT027084.1|DT027084
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71880570|gb|DT029625.1|DT029625
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71879450|gb|DT028505.1|DT028505
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71877779|gb|DT026834.1|DT026834
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71879745|gb|DT028800.1|DT028800
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|110700156|gb|EE077872.1|EE077872
EST:     AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71878345|gb|DT027400.1|DT027400
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|351014558|gb|FQ437560.1|FQ437560
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|351034081|gb|FQ447999.1|FQ447999
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71877851|gb|DT026906.1|DT026906
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|110417025|gb|EC983046.1|EC983046
EST:     GGCGACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: GGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71877603|gb|DT026658.1|DT026658
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|37188912|gb|CF608261.1|CF608261
EST:     AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|110360137|gb|EC922817.1|EC922817
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71890445|gb|DT039500.1|DT039500
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTG
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTG
EST: gi|71880590|gb|DT029645.1|DT029645
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71880998|gb|DT030053.1|DT030053
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|110408342|gb|EC973977.1|EC973977
EST:     AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71879800|gb|DT028855.1|DT028855
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
EST: gi|71880385|gb|DT029440.1|DT029440
EST:     AGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACTTTTGGCCAT                         GCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT
genomic: AGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttg ... ttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaaagaaacccctttaagcaatcccattctgattatcacatcttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG
                             ttctgat  putative branch site (score: 3)
                                      tcacatcttttcttc  putative PPT
                                tgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatcttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
-tggtttg
- - - - - - - - - - - - - - - - cccatgt
- - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttt