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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatatatattcattgtgtgcattgacattcattactttttgtgataattgtgattattgacatatatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 9
---------------------------------------tatatatatattcat-tgtgtgcattgacattc-attactttttgtg----ataattgtgatta---ttgacat-atatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC
                                       |  || |   || ||     || | | | |||  | | || ||  ||    |  | | ||| ||   ||   || ||| |  |||||   | |||   |   || ||||||| |||||||||||||||||| | ||||||||||| || ||||| |  || || || | |||  | ||||| |||||||| ||  |||| ||  || | |
gtatctatcactttgcacagttttcacaatttttttacttgcatttccctttatgcacttggaattatattttagtgctgttcatgtacaaccagtatgaatacacttctgatgatactcatttgtacttggtattgtgctatatgcagGTCCAGCATCTTATTGCAGAACTAAATGAAATTCTTGCCCATGATACTGTGGATGAGGGTGGGTTATGGAAGAAGAAACTCACTGATCAATCATTGAAGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 7
--------------------------tatatatatattcattgtgtgcattgacattcatt-actttttgtgataattgtga----ttattgacatatatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC
                          | | | | |   |||    ||  ||| |||   || |  |    | |  || |  |    ||| |||   ||  |  |   ||   | | |  |||   |||||||| || || |||||||||||| | |||||||||||||| ||||| |  || || || |  || || ||||| |||||||| ||  |||||||  |  | |
gtagctatcactagtcgttaatagtttttttttctccccatatgatgttttggcatctgttcatgtacaatcaatatggaaacatgttaatgaataatgatggtcacttttatattcttttttgcttgcagGTCCAACACCTTATTGCAGAACTCAATGAAATTCTGGCCCATGATACTGTGGATGAGGGAGGGCTATGGAAGAAGAAACTCACTGATCAGTCATTAAAGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 9
------------------------------------------------tatatatatattc---attgtgtgc-attgacattcat-tactttttgtgataattgtgattattgacatatatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC
                                                    | |  | |    ||| |||   | ||   ||||| |||    ||| || | |    ||  |||   ||| |  |||||   | |||   |   || ||||||| |||||||| ||||||||| | ||||||||||| || ||||| | ||| || || | |||  | ||||| |||||||| ||  |||| ||  || | |
gtatctatcactttgcagttttcacaattatttttttacctgtgtttccccctctgcacttgggattatgttttagtgttgttcatgtacaacctgt-atgaatacactt-ctgatg-atactcatttgtacttggtattgtgctatatgcagGTCCAGCATCTCATTGCAGAACTAAATGAAATTCTTGCCCATGATACCGTGGATGAGGGTGGGTTATGGAAGAAGAAACTCACTGATCAATCGTTGAAGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 9
------------------------tatatatatattcattgtgtgcattgacattcattactttttgtgataattgtgattattgacatatatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC
                        | | | | |   |||    ||  ||| |||   ||    |       |  ||  |  |   |   ||  |  |   ||   | | |  |||  ||||||||| || || |||||||||||| | ||||||||||||||  ||||    || || || |  || || ||||| |||||||| ||  |||||||  |  | |
gtagctatcactagttgtcaatagtttttttctccccatatgatgttttggcatctgttcacgtacaatcaatatggaaacacctattaatgatggtcacttttatattcttttttgtttgcagGTCCAACACCTTATTGCAGAACTCAATGAAATTCTGGCAAATGACGCTGTGGATGAGGGAGGGCTATGGAAGAAGAAACTCACCGATCAGTCATTAAAGC

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|161710861|gb|FC058565.1|FC058565
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|87583926|gb|DY473286.1|DY473286
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|161717766|gb|FC066590.1|FC066590
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|37183710|gb|CF603064.1|CF603064
EST:     ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGANATTCTGGCTCAT
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCAT
EST: gi|110699977|gb|EE077493.1|EE077493
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|110730531|gb|EE107719.1|EE107719
EST:     ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|71865073|gb|DT014128.1|DT014128
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAA
EST: gi|110730571|gb|EE107799.1|EE107799
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|77584856|gb|DV221506.1|DV221506
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|161714537|gb|FC062987.1|FC062987
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|71857501|gb|DT006556.1|DT006556
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|161719694|gb|FC067068.1|FC067068
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
EST: gi|27581975|gb|CB004670.1|CB004670
EST:     ACTATGGTGTTATACTTATTCCGGAAGGCCTTATTGATTTCATACCTGAG                         GTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA
genomic: ACTATGGTGTTATACTTATTCCAGAAGGCCTTATTGATTTCATACCTGAGgtataatatt ... tcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattgtgattattgacatatatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC
                                           tttcattt  CT-rich tract
         attattgacatatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatatatattcattgtgtgcattgacattcattactttttgtgataattgtgattattgacatatatttttttgttgattgtacaatttcatttgcagGTGCAGCATCTTATTGCAGAATTGAATGAAATTCTGGCTCATGAAATCGTAGACGACGCTGGCCTCTGGAAAAAGAAACTTACAAATCAGTCTCTGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - -tgcattg
- - - - - - - - - - - - - -cattcat