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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgctattataatacttctctatattcaactccataaagccccccaaactgaaatttattctgctgtttcccaagttctaactataaaatggtaacatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTAATGGAAGACAAAAAGAGCCTTGCTTCTTCAGATGAACGAGCCCAAATTA

Basic information

species Vitis vinifera
transcript Vv00s0313g00030.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 8
------------------gttgctattata-atacttctctatat---tcaactccataaagccccccaaact--gaaatttattctgctgtttcccaagttctaactataaaatggtaacatgtc-cagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTAATGGAAGACAAAAAGAGCCTTGCTTCTTCAGATGAACGAGCCCAAATTA
                   |||  |   || | |||  |  || |   | |  ||    |    |   ||  |  |||||| ||| || |  ||||   ||| ||| | |||  ||||    | |  ||||| |||||||| |  || ||||||||||| || || ||||| ||||| || ||||||||||| |||||||||||||| || || || ||  | || || |
gtaaaacatgttgcttggtttgacacagtagagactcattcatctgaattagttcttgtattttctataatttaggaaattgattatgtt--ttccttggttttaagt-taagttggttgtgtttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCTGATGGAAGACAAGAAGAGCCTTGCTTCATCTGAAGAGCGTTCTCAGATAA

upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 8
---------gttgct-attataatactt------ctctatattcaactccataaagccccccaaactg-aaatttattctgctgtttcccaagttctaactataaaatggtaacatgtc-cagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTAATGGAAGACAAAAAGAGCCTTGCTTCTTCAGATGAACGAGCCCAAATTA
         ||||||   | | | ||        || | |||||| ||  || |   |    |   || ||| | ||| || |||  ||    || ||| |  ||  ||||   || |  ||||| |||||||| |  || ||||||||||| || || ||||| ||||| |  ||||||||||| |||||||||||||| || || || ||  |  | || |
gtaaatcatgttgcttggtttgacacagtagagactttttattcatctgaattagtgcttgtattttgtaaagtgattatgttgt--ccttgtttttaagtg-aagttggttgtatttttcagGTCTATGGTGGAGAGGCAAGGATTTCAACTTTGAGGGAATTATTTCCTCGGATGGAAGACAAGAAGAGCCTTGCTTCATCTGAAGAGCGTTCTGAGATAA
















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|30322447|gb|CD005709.1|CD005709
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|18459384|gb|BM437662.1|BM437662
EST:     CAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|71857949|gb|DT007004.1|DT007004
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|161710023|gb|FC060239.1|FC060239
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|32267466|gb|CD716429.1|CD716429
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|30301036|gb|CB977830.1|CB977830
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|110703560|gb|EE080515.1|EE080515
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAA                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|37188131|gb|CF607482.1|CF607482
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|351034043|gb|FQ447960.1|FQ447960
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|30326708|gb|CD009970.1|CD009970
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|32267671|gb|CD716634.1|CD716634
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|32247339|gb|CD713158.1|CD713158
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|32268570|gb|CD717729.1|CD717729
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|29786039|gb|CB343476.2|CB343476
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGGGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|32270504|gb|CD719663.1|CD719663
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|71871778|gb|DT020833.1|DT020833
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|71876785|gb|DT025840.1|DT025840
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|161720195|gb|FC066766.1|FC066766
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|32267988|gb|CD717147.1|CD717147
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|30325113|gb|CD008375.1|CD008375
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
EST: gi|30324596|gb|CD007858.1|CD007858
EST:     CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAG                         GTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA
genomic: CAGCTTTGGGCTTTGACAACACTACTCGACTATACCTTGCCTCCCACAAGgttgctatta ... acatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatttattctgctgtttcccaagttctaactataaaatggtaacatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTAATGGAAGACAAAAAGAGCCTTGCTTCTTCAGATGAACGAGCCCAAATTA
                          ttctaactataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctattataatacttctctatattcaactccataaagccccccaaactgaaatttattctgctgtttcccaagttctaactataaaatggtaacatgtccagGTGTATGGTGGGGCAGCCAGGATTTCAACGTTAAGAGAATTGTTTCCACTAATGGAAGACAAAAAGAGCCTTGCTTCTTCAGATGAACGAGCCCAAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG