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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG

Basic information

species Vitis vinifera
transcript Vv15s0021g02230.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 9
gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatcttt----gcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
  ||  | | |  |  |  |   ||  ||||||  |    |   ||||| | ||    ||||   ||     |     ||   || |  ||  |||    |||||||| |||| || || || ||||||||||||||| ||||||| ||||| || |||||||| || || || || || |||||||| ||| |||| |||
--tttatttctattgttttgtggaatgtggttggatc-cacacataattctattata-atttatggtctccaattgtaaaacataatcttacttttcatggcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTACTGACCACTAAGGGAATTGATGATATGTCACTGAAG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 7
-----gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
        | |  ||  ||   ||    ||       ||||    | | ||||   |||| ||  |      | |    ||       | ||  | |  |  ||||||| |||| || || || ||||||||||||||| |||| || |||||||| ||||||||  | || || || || ||||| || ||| |  | |||
ttcctatatctgatagaatcagcactgtaaacacacagtctg--ccatataatctatttgaggtctcaa-acgttcatccatgtttcttgctctttttct--cagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 9
---gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
   | ||| | |  ||   |   | |   ||       |      |  | | || | |  |||    | |||   |   | |  |    || | |  ||||||||| |||||||||||||| || || ||||| ||||| ||||| |||||||| |||||| |||| || || ||||| |||||||||||||| ||||||
tttgcttggtttgggacaattctccatccatatcatcttgcaagataaagtaatatcgatgatacattttgacaaatggccattt---tttttctaattgcagAGAGGCTGATATGACTAAGGAACGTATTGAAAAACTGCTGAAGGCTGGAGCTAATGTTATTCTGACAACTAAAGGAATTGATGACATGGCTCTTAAG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 9
gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatcttt------gcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
     || |    |  |  | | ||  |     || |  || | |    || |   | | |  || | ||  |     |  ||  | | | | |||      ||||||| || ||||||||||| || || ||||| ||||| ||||| |||||||| |||||| |||| || || ||||| |||||||||||||| ||||||
-----ttttgctttgtttgggacaat-tctccatccatatcatcttgcaatataaagtaatatctataatacattttgacttgggcctttttttttctaattgcagAGAGGCCGATATGACTAAGGAACGCATTGAAAAACTGCTGAAGGCTGGAGCTAATGTTATTCTGACAACTAAAGGAATTGATGACATGGCTCTTAAG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 9
-gattgttctatgattct-cagcaaaagatggttgtctaattcttgtaat-tattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
 ||  | |  || | | | |   |    |   ||||  |  || ||| || | | ||    |     | |  |       |  ||| |  | | | |   |||||||||||| ||||| |||||||| || ||||||||||| |||||||| ||||||||  |||| || ||||| |||||||| |||||||||||||| 
ggaaagcttaataaatttgctttactgtacacttgt--agctcatgttatctgtgttccatacagagttttttaatatgttg-ctgaatatttgtttccacagAGAAGCTGACATGACAAAAGAGCGGATAGAGAAACTTCTCAAAGCTGGGGCCAATGTAATTCTGACCACAAAGGGGATTGACGACATGGCACTTAAA

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S97_11V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------gattgttctatgattctcagcaaaagatggttgtctaattcttgtaa---ttattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
                                                                                            ||  || |   |  |  |   |  ||||   || | || |   |||    |  | |  || |||  | ||||  || |  ||||| |        | ||||| ||||| || || || |||||||||||||||||| | |||||||| || || |||||  | || |||||||| || |||||||| |||||  | |||
gtaaatactcggttgacatcgtgtgcagtgttttctgcagcacatatttttgccttctcaacgtgcattcttttgtttctatacgtctataaatgtttttgcaacgcaaatacattgatgaaagttttatcccaataagatctcgtctctggttttaatttgatcaagta--aactgca--------tctgcagGGAAGCAGACATTACCAAAGAGCGAATTGAGAAAATCCTGAAAGCAGGGGCAAATGTCATCCTTACTACAAAGGGTATTGATGATATGGCTTTGAAG

upper sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagc--actaactgta-cttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
   | |  |  |    |   ||   |||  || |||  |  || |  |||||  |   |     | |  |    |  | |     || || |||  ||||||| ||||| || || ||||||||||||||||||||| |||| || || || || |||||  |||| ||||| || || |||||||| ||| |  | |||
---tatattggggagtttgtcacgggatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG

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|110719721|gb|EE095097.1|EE095097
EST:     GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|351037610|gb|FQ462593.1|FQ462593
EST:     GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|351017726|gb|FQ436079.1|FQ436079
EST:     GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|37187670|gb|CF607023.1|CF607023
EST:     GCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|71882935|gb|DT031990.1|DT031990
EST:     GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|30322269|gb|CD005531.1|CD005531
EST:     GTCCAAGTATTGGTCACTGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|110688105|gb|EE066273.1|EE066273
EST:     GTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
EST: gi|351048864|gb|FQ431529.1|FQ431529
EST:     GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAG                         AGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC
genomic: GTCCAAGTATTGGTCACCGATCCAAGGGAGCTTGAGAAAATTCGTCAAAGgtgatcagtt ... atctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG
                             cactaac  putative branch site (score: 1)
                                            tatcttt  putative PPT
                                         ttatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG

- - - - - - - - - - -aaaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactaac