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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT

Basic information

species Vitis vinifera
transcript Vv13s0019g02280.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 5
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctat-tgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
                                                                           | ||| ||   |||   |   ||   ||  |  |  |  |   || | |  || | | ||  |   | ||       || | ||| || ||| ||||||| |||| ||||| ||||||||||||||||| || || || ||||||||||| || ||  |||| || |  || ||||| || |||||  | ||||||||
---------------------------------------------------------------------------gtaacttatattgggcgtt--tactgctgtattctcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagcttcagATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACCTTGTGT

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctat-tgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
                                                                           | ||| ||   |||   |   ||   ||  |  |  |  |   || | |  || | | ||  |   | ||       || | ||| || ||| ||||||| |||| ||||| ||||||||||||||||| || || || ||||||||||| || ||  |||| || |  || ||||| || |||||  | ||      
---------------------------------------------------------------------------gtaacttatattgggcgtt--tactgctgtattctcttcacactcaactaggttaggtaagcatgctgatcagcgaaatattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggta--ctcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
                                                                                        |||  ||   |||| |   | | ||  ||  || |    | ||| |  |   ||| | |    | | || | | || ||  ||||||| | || ||||||||||||||||| ||||| || || ||||||||||||||||||||  | || || |  || || ||||| |||||||| || ||  |
----------------------------------------------------------------------------------------gtaacctgcatatgtcattatgacactgacatt-tgccctataaggatatttactgactaaaatattttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
gtaaatccatgaaatcttggattgtt-gtc--cctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
    ||  |    ||  |||  | || |||  |||| | || |  ||| ||  ||  |  |||      |    | ||      | || ||   |  |   |   |    || ||||||| ||  || || |    || | |  | ||   || || | || |   ||||||||||| | |||||||||||||||||||||||||| ||||| ||||| || |||||||||||  | ||||| ||||| |||||||||||||  || |||||| |
--gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactt---tttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaat-tttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
gtaaatccatgaaatcttggattgtt-gtc--cctaagcctcagttttaattcatagttctt-tttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
    ||  |    ||  || | | || |||  |||| | || |  ||| ||   |  || |  | | || |||| | ||      | || ||   |  |   |   |    |  ||||||| ||  || || ||   || | |  | ||   || || | || |    |||||||||| | |||||||||||||||||||||||||| ||||| ||||| || |||||||||||  | ||||| ||||| |||||||||||||  || |||||| |
--gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatctt---ttggttgaagcagaactt---tttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaat-tttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G07160.1 (Glycine max), 3'ss of exon 5
--gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttccccca-agtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
    |   || |   ||   | ||| ||   | |||  || || ||| ||  ||  | || || |  |||||       | | | |  ||||              ||||| ||  |    ||||  |||  |     | |||||   ||   | | |||  |  | ||||||||||   |||| |||||||| |||||||||||| ||||| ||||| || |||||||||||| | ||||| ||||| ||| ||||||||| ||| |||||| |
gtacaggacctttttatggagtatttttacacataaatctaagattttatgtatgttactcttcccattgtg------tagcgtggtttggtt-------------gaagc-atcaa----ctatgatgtcta-----agacttatcattgattctagttttctgagagtttcagATACAGGACTGGTGTGGGCTTGGGGCTATGGAGGTGAAGGGCAGCTTGGTTTGGGTTCCAGAATACGCATGGTTTCCACTCCTCATCTTGTTCCTTGTAT

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G41810.1 (Glycine max), 3'ss of exon 5
--gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttccccca-agtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
      | || |   ||   | ||| ||   |||||  || || ||| ||   |  || | || |  |||||       | | | |  ||||    ||||| ||    | | |||  | |||||              | |||||   ||   | | |||  |  | ||||||||||   |||| |||||||| |||||||||||| ||||| ||||| || ||| |||||||| | ||||||||||| ||| ||||||||| ||| |||||  |
gtacggaacctttttatggagtatttttacacctaaatctaagattttatctgttattttcttcccattgtg------tagcgtggtttggt-tgaagtatcac----aactatg--acttcta--------------agacttaccattgattctggttttctgagagtttcagATACAGGACTGGTGTGGGCTTGGGGCTATGGAGGTGAAGGGCAGCTTGGTCTGGGTTCCAGAATACGTATGGTTTCCACTCCTCATCTTGTTCCTTGCAT

upper sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttcta-ttgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
         ||| || ||    | ||  | |      ||| |  | |   | | ||  || ||  || ||   |    |     |  ||||  || || |   |  |||  | |  || ||||       |  ||  | ||| |||  | ||| || ||   |  |  | ||||| |||||||||||||||||||||| ||||| || || || || || || ||||| || ||  ||||| | || ||||||||||||||| | || ||  |
--------gtgagatttttagcttttcacacaccatgtcactaatgaggtaca-ttggttatcaattatgaaaaaaatatcagtggcggtatccattaagctaaagagcttttggtgtgctat-------aataatca-cttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT

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|110385026|gb|EC949508.1|EC949508
EST:     GAGGATTGCTAATGTTGCTGCTGGCGGGCGTCATACTTTAGCATTGTCAG                         ATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTT
genomic: GAGGATTGCTAATGTTGCTGCTGGCGGGCGTCATACTTTAGCATTGTCAGgtaaatccat ... caagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT
                     acttaat  putative branch site (score: 4)
                             ttttctattgttcccc  CT-rich tract
                       ttaatgttttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatccatgaaatcttggattgttgtccctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC