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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA

Basic information

species Vitis vinifera
transcript Vv10s0003g04670.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 11
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcact----attgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
                                                        ||     | |  | | ||    ||  ||    |||   |         |||  ||||  ||   | |   || ||   |    ||  ||  |||     |  | | || | | | ||| | | |   || ||||||| || |||||| ||||||| ||||| ||||| || || |||||||| ||||||||   |||||||||||||||||||||||| | | |   ||| |
-------------------------------------------------------gttgacataggctctattt--agttgctcagctaattatagattgtctctatc-tttgtttcactttgaccaaaattgttccaaatcaaagaattaagctttacaaaatgtcattttttttataa---tgtagAATGTACCTCCTGCTCTACTTGTGCGATTTCTGAGGGAGCATCGTTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTTCTTTGCGAGCCA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g43930.1 (Oryza sativa), 3'ss of exon 11
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcacta-ttgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
                                                                                           | |    | || |    || |   |  |    ||   ||| | || ||||  | |||  |||  ||  |   |  |||||   | | | || ||||||| || |||||| | || || |||||  |||| || ||||| ||||| ||||||||   ||||||||||||||||||||||||     | |  ||||
-------------------------------------------------------------------------------------------gtctttactcataatccatctaggtaattattgt--gcatgagtagttgagttgtttattatgacctgacaagcttgttt---tcattgtgtagAATGTACCACCTGCTCTCCTAGTGCGATTTTTGAGGGAGCACCGCTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTGCGTTGAGGGCTA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 10
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggat-gtccaacttctgttttatctctcaatgccaccccacaaatattatttgaa--tcttctgggttaacatcactatt--gaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
           || |  |||  |    ||  | | ||   ||      ||   ||  |||| |    |  | || ||  | | | |  || | | |    |  ||| ||  | | |  | | || |  ||| |||  | ||  |  ||| || |  |  ||  |    |||  ||   |||   || ||||||| || |||||| ||||||| |||||  |||| || || || ||||| |||||||||  |||||||||||||||||| ||||| | ||| |  || |
-----------gtttgtacatgcactcaat-tttgttccaagc-----tactttaccttgtagtccatttagctgcttgtgt-tgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgtttttatggtatagttaaccttgccccaatgtacttctt--ctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 11
gtacataga--aagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgtttt-atctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
||||||  |  |  ||||   |   |   |   | || |  || | ||| | |  ||||||    ||| | || | || ||||  | || ||||      |   ||  ||  | | ||| ||||   | | ||||  ||||| |       || | ||                      ||| |||||||||||||||||||| |||||||||||  |||| || || || || ||||||||||| ||||| |||||||| || ||||||||||| ||||||||||
gtacatgaaacagttctatggactatgacataatataatattaat-aatat-taataatttc--aatgccaaattcctctttttgtttcccaat-----tcgtgaagcatcttctaaattttctctataatcatc--tattgta-----caatgtgtc----------------------tctacagAATGTTCCCCCTGCTTTGCTTGTTCGATTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCTGCATGCCTTAAAGCTA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 11
gtacatagaaagtctagacaaccttgtaaggtctattgatag-tgaatgtatgctaatttgtggatgtccaacttc---tgttttatctctcaatgccacccca-caaatattatttgaatcttctgggttaacatcactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
|||| |   |   | |  | |  | | ||     |||| |   | |||  |  ||| | |         ||| | |     || |  |||  | || | || |  |  |  ||  | ||||||||||| ||    | | | || |  | ||   ||||   |  |   |      ||     ||||||||||||||| |||||||| |||||||| || ||||| || || ||||| ||||||||| | ||||| |||||||| || ||| |||||||||| |||||||
gtacttctcagacc-aatctatgtggaaattatcattgttctctaaattaactctagtattgtagcaatcaattccgagaattcttcctcctagtgtccccacgtcccaacttgctagaatcttctggattt-tgtaattgttca--tcttcattatacttaattacaaa-----atggtggtctgcagAATGTTCCTCCTGCTTTGCTTGTTCGTTTTCTGAGGGAGCATCGTTCAGAGTGGGCTAATTATGGGGTTGATGCATACTCTTCTGCATGTCTCAAAGCTA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 11
gtacatagaaagtct-agacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcactattgaaatatttgatatatccatatctgactgtttatttg-aatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
       | |  ||| |||| |   | |  |        |||||    | |    ||||    ||  |||  || ||    | |  | | ||| |  || ||     ||  | ||||||||||| ||          ||| | | |||    |    |||    | | |  |   |   ||||||||||||||| |||||||| |||||||| || ||||| || || ||||| ||||||||| | ||||  |||||||| || ||| |||||||||| |||||||
-------gtacttctcagaccaatctatgtgactctagtatagtagcagca-atcaattccaagaactcctcctcct----tgttcccccatgtc--ccaac-----ttgctagaatcttctggattt---------ttggagtgtttatcttcattatactcaattataaaacggtggtctgcagAATGTTCCTCCTGCTTTGCTTGTTCGTTTTCTGAGGGAGCATCGTTCAGAGTGGGCTAATTATGAAGTTGATGCATACTCTTCTGCATGTCTCAAAGCTA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 11
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacat-cactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
                                       ||    |   |     ||  |   | |   ||  |   |  |||   |  || | |  | | |  | |  |||   | | ||   ||   |  ||   |  |||| ||    |||  ||| |||       | |||   ||| ||||||||||| |||||||| |||||||| ||  |||| || || || || ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||||
--------------------------------------gtacctgaaacaattctatgggctcaggcataatgttaataatattaatatatactattcaaaatttgtctttttg-tttcctaatttgctaagcatcttctaaattttcatcataatcatctcttgtacaatgtttc--tctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
                                                                              |  || ||| || |  |    | ||  |  |    ||| |||||  ||    ||  | |  || ||  |   ||            || ||| |||   | || |||| ||||| || ||| | || ||||||||||| ||||||||||| ||||| |||||||| ||||| || ||||||||| |||||||||  || | ||| |
-----------------------------------------------------------------------------gtacatgtcttaagg--atttgataataaaaaaactaatattctg--tttctgtctgtttctaactaacttgcat------------ctttttttttttgtttgaagAACGTTCCACCCGCTGTGCTGGTTCGATTCCTTAGAGAACACCGATCTGAATGGGCTGATTATGGCGTGGATGCTTATGCTGCTGCATCGCTCAGAGCAA

upper sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcactattgaaatatttgatatat--ccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
                                                                                                 ||   |  ||  |||||  ||| ||  |  |||  |  |  |   | ||  || | |  |   ||     | ||||| ||    || |||||||||| ||   | || |  |||| |||||||||||||||||  |||| ||||| ||||||||||| ||||| ||||||||||||| ||| | ||| |
----------------------------------------------------------------------------------------------gtgcctatatcatgttttgacacttgtgaatagacaaaagaaccggtttcttcaatttctgacatcattctcttttttatctgctcttgaagAATGTTCCACCCCTTGTATTGATTCGGTTCCTGAGAGAACACCGAGCTGAATGGGCAGACTATGGTGTCGATGCCTATTCTGCTGCATCTCTCAGAGCAA

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|30256255|gb|CB972098.1|CB972098
EST:     CAACTTTCGGAGGTGGCGTGCTGTGTGCCAAAGCATCAATGCTGCTACAG                         AATGTTCCTCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAG
genomic: CAACTTTTGGAGGTGGCGTGCTGTGTGCCAAAGCATCAATGCTGCTACAGgtacatagaa ... gaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA
                             atctgac  putative branch site (score: 3)
     tattgaaatatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacatcactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC