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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctgattttgtgggtcttttacctgctttcatcatttgtttttgattgacaatgctcttagtctctgcataatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA

Basic information

species Vitis vinifera
transcript Vv17s0000g09390.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G08770.1 (Glycine max), 3'ss of exon 4
ttttctgattttgtgggtcttt-tacctgctttcatcatttg--tttttgattga-caatgctcttagtctctgcataatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
   | | |||| |    | ||| |   |  ||| || |||    | ||  ||  |  | ||   |||    |||     |||   | ||  ||     ||| ||||| ||||| | |||||||||||| ||||| || |||||||||| ||||||||||||||| || || ||||| ||||| | ||||||  ||||||  || 
--atgtaatttagataatatttatttatatttttattattaagatcttcaatcaaatactgtagttaaggcctgagctctgggtta-tgtttgaactgtgataGGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAGAAGGGCCAAACTCTACTATCTGAGGGAGAGAATGAACCCACTTAAAAA-

upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G34520.1 (Glycine max), 3'ss of exon 4
ttttctgattttgtgggtcttttacctgctttcatcatttgtttttgattgacaatgctcttagtctc--tgcataatggccaa------atgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
      |     |||    ||||   ||||   ||  ||  ||     ||||   ||||  ||||     | ||||||||  ||      ||   ||     ||| ||||| ||||| | |||||||||||| ||||| || |||||||||| ||||||||||||||| || || ||||| ||||| | ||||||  ||||||  || 
------ggggcggtgtaatttttttgtgctggaatttttaattc--agttgattgtgcttgtagttatattacataatggttaatgccttatatttgaactgtgatagGTATTCACCTAACATAAAGGAGATAAAGGTGCTTGACAAGAAGAGAGTGAGAAGGGCCAAACTCTACTATCTGAGGGAGAGAATGAACCCACTTAAAAAT

upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G11630.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------ttttctgattttgtgggtcttttacctgctttcatcatttgtt--tttgattgacaatgctcttagtctctgca--taatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
                                | ||||  |||| |   |||   |  |  | | || || || |   |  |   || ||| | |  ||  ||  |  | |||       | |||  || ||||||||| || || | | | | |||||| |||||  |||||||||||||||| ||||| |||||||| ||||| |||||||||||  ||||||| |||| ||| 
gtaagtaacttgaagctcaaactgcaactacttattctttttttctttctctcagaatttgtat-atgatatgataactcaagccaccatgttttgtgtgccttaaattgatgtgagtgagggtgtttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTATATTACCTCAGGGACAAGGTGAATGCTCTTAAGAAG

upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G11750.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------ttttctgattttgtgg---gtctt-ttacctgctttcatcatttgtttttgatt-gacaatgctcttagtctctgcataatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
                                   |     |   || ||    |||     |||   ||| ||   || | |||| || |   ||| |   |         | |  |     ||  ||  || ||||||||| || || | | | | |||||| |||||  |||||||||||||||| ||||| |||||||| ||||| |||||||||||  ||||||| || | ||| 
gtaagtacttttgtctatttctctcggtaagaccatcaagaggcattatgataagtcaagccaccgagttttatgtgttctctttgctttggtcatggtgaaaaaactgatgtgagtga-gggtgtttgtttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTCTATTACCTCAGGGACAAGGTGAATGCTCTCAAGAAG

upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G24240.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------ttttctgatt-ttgtgggtcttttacctgctt-----tcatcatttgtttttgattgacaatgct---cttagtctctgca--taatggc-caaatgagtgcg---tgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
                                                             | | |||   ||  | | | ||    |  |       || ||| | || |   ||  |  || |   ||| |||   | |  || ||    || ||   | |   || ||||||||| || || | | | | || ||| |||||  |||||||||||||||| ||||| |||||||||||||| |||||||| ||  | ||||| || | ||| 
gtaagtaacttcaagcttcaagcttgtgcagccactttaatctttttctctcagacttttgtatatgaccattaagagccattattataatcaagagccaccatgttttgtatgttctctttgtttgccttggtcatggaaaatactgatgtaagtggaggtgttttggtgacagGTATTCCCCAAACCTGAGGGTGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTTTATTACCTCAGGGAAAAGGTCAATGCTCTCAAGAAG

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|349827639|gb|FQ422507.1|FQ422507
EST:     AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACT                         GTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
EST: gi|349825024|gb|FQ415571.1|FQ415571
EST:     AGATTAAGGAAGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACT                         GTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
EST: gi|110382393|gb|EC939358.1|EC939358
EST:     AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACT                         GTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
EST: gi|110381353|gb|EC946681.1|EC946681
EST:     AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACT                         GTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
EST: gi|349829899|gb|FQ422212.1|FQ422212
EST:     AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACT                         GTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
EST: gi|110703698|gb|EE080772.1|EE080772
EST:     AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATNCCTTTTTCCACT                         GTACTCACCCAGCATAAAAGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
EST: gi|110385492|gb|EC950024.1|EC950024
EST:     AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACT                         GTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG
genomic: AGATTAAGGAGGCTGGTAGCAGGGGTGGGGGTTGAATCCCTTTTTCCACTgtaagttaat ... gtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgacaatgctcttagtctctgcataatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
 gattgac  putative branch site (score: 3)
                          ataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctgattttgtgggtcttttacctgctttcatcatttgtttttgattgacaatgctcttagtctctgcataatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - ttgtggg
- - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaaatg