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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggacagacttatcaggctaactccatggtgacgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
tttggacagacttatcaggctaactccatggtga--cgacttttaaattttgatcttgttatcttactttgtaagactgatttg--ttaaat---tgttatgt---tcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
        | |||| |   ||||||  | | |||  | | || ||     |   | ||| ||   | ||  ||  | |   |||  | ||||   |||||      |||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||
-------tggcttaac---ctaactgaaagatgatacaatttgtagcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgttactcatgtcagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 6
---tttggacagacttatcaggctaactccatg-gtgacgacttttaaattttgatcttgt-tatcttactttgtaagactgatttgttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
    ||   |  ||| |  | | | |  | ||  ||  | | | |  |  | ||||    | | |     |||||  | || |  |||    |  | |||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||| ||||| |||
tgacttaacctaactga--aagatgatacaatatgtagcaaatat--acctgtgatgccatctgttactatttgttgggctcaaatgtatgttactcatgt-cagGTGAACCCGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
tttggacagacttatca--ggcta-actccatggtga-cgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaa--attgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
      || || |   |  | ||| | |   |  | | | | | ||     ||| | || |||    |  || ||    |   ||   |   ||||| |||| |||||||| |||||||| |||||||||||| ||||||||||||||||||| ||||| |||
----accatacctgcaattgactagaatttgtcataaacaaatgttg--ccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G09840.6 (Arabidopsis thaliana), 3'ss of exon 6
--tttggacagacttatcaggctaact--ccatggtgacgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
   ||  | |  || |  ||    | |  | ||    |    | ||   | || || |   |   ||    | ||   |||| ||   | ||  |  ||| |||||||||||||||||||||||||| ||| | |||||||| |||||||| ||||| |||
agcttaaaaattctaactagttagaattgctatctaaaaagttgttcggtgttaatttaaatgcatt----tatatatctgactttacagatgttgttgtgcagGTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------tttggacagacttatcaggctaactccatggtgacgacttttaaattttgatcttgttatcttactttgtaagactgat-------ttgttaaattgttatgtt---------cagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
                                                                      | | |     |  || |  |   |  | | ||   |||   |  ||| |     || |    |   |  | || |          | || | |   || ||||         |||||||| || || ||||| ||||||||||| ||||||||||| |||||||||||  ||
gtacgtgtgtccgacgaatcttgtcatgtgttcaagtatcttgaaaacacgatgctgactgtttaagcactcgtatttgttgctcggcatgggtggaagctggttactgagatgtttggtatgagtcacgggaaagtacaggagttgccgtggtgtcgtaacaaacttgtgtttgcatggcacagGTGAATCCTCATACGCACCAGCTGAAACTGTGTGATTTTGGAAGTGCGAAAGTGCTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------tttggacagacttatcaggctaactccatggtgacgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaaattgttatgtt-cagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
                                                                            | |   | || ||        |   |||     ||||   | ||     | | |   | | |     | | |   |||   |     ||  |    | |||||||| || || |||||||||||||| ||||| |||||||| || ||||||||| ||
gtaagtgaatgctggtgtatatgtgatggacttaagcacatggatggtgagcatagtttagcaccgacaactattatgtcaccggagtttgtgaataagggccagatgtacgagcgtcaagg--agttgtgagtgtatggaagtatgatgatgacgaggccggtttgtgcactgcagGTGAATCCTCATACGCATCAGCTGAAGCTTTGCGATTTTGGTAGCGCGAAAGTTCTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------tttggacagacttatcaggctaactccatggtgacgacttttaaattt-tgatctt------gttatcttactttgtaagactgattt-------gttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
                                                     ||  ||| |||   |  ||     |  | |  || ||  ||| | | | ||| | |      ||| ||    | || |||  || |         |||   ||||   || |||||||| || |||||||||||||| || || || || ||||| |||||||||||||||
gtaatattgtgttgtgagtattagtatgtaaatatggtcgactcgagcacagtttaagaccgacagttgtggtattattgaggtggatgaggtttgattgtatgagcatcgaggagttgtcaaggtgtggaagtgtggtgatgaagaggttggtttgtgtggtgcagGTGAATCCCCACACGCATCAGCTAAAGCTATGCGACTTTGGAAGTGCGAAAGTTTTG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------tttggacagacttatcaggctaactccatg--gtgacgacttttaaattttgatcttgttat--cttactttgtaagactgatttgttaaattgttatgtt-cagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
                                                                           ||  |||    |||       || | | ||  | |     | ||||     ||  |||  |   |||     ||        |  ||| | || || ||   |||||||| || || |||||||| |||||||||||||| ||||| || || |||||| ||
gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaagagcttgaacggtgttgtaactgggttgagtttttgtggcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG

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|46917752|gb|CN547081.1|CN547081
EST:     ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT                         GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
genomic: ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTTgtaagattct ... ttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
EST: gi|110726124|gb|EE101641.1|EE101641
EST:     ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT                         GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
genomic: ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTTgtaagattct ... ttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
EST: gi|161715603|gb|FC067769.1|FC067769
EST:     ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT                         GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
genomic: ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTTgtaagattct ... ttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
EST: gi|156736132|gb|EV240253.1|EV240253
EST:     ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTT                         GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA
genomic: ATAATTGCATTGGTATTTGTCACCGTGACATCAAGCCTCAGAACTTACTTgtaagattct ... ttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgatcttgttatcttactttgtaagactgatttgttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
                           gactgat  putative branch site (score: 3)
                                atttgttaaattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggacagacttatcaggctaactccatggtgacgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaaattgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - -caggcta
- - - - - - - - - - - - -ccatggt