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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC

Basic information

species Vitis vinifera
transcript Vv09s0054g00890.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 11
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
         | |  | || ||||| |   ||  | |  ||||  | || || ||| |  | || | |  | | ||| || |||||||||| ||||| ||||| ||| | || |||||| | |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||| ||||
--------gtatgctttcctttcatttgcaaatattgtgtttcta-attttagagttggtcaaactaattcaatga-ttgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 11
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
|  |||  | || |||  ||     |   ||  | |  ||||    |  ||  || |  | || | |  | | ||| || |||||||||| ||||| ||||| ||| | || |||||| | |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||| ||||
gcatgttttatt-ttcagttacttctatcaaatattgtgtttct-tagtttacagttggtcaaactaattcaatga-ttgttcagGTTCTAATGGACTTTCCCCAACTTACAATGACATTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGCACAACACTAGTGGCTAACACTTCAAACATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G78900.1 (Arabidopsis thaliana), 3'ss of exon 12
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
    ||   | ||||||| ||  ||   |    | |  |||   |||  | ||| ||||    |    ||| || | | | | ||||||||||||| || || |||||||| |||||  |||||||||||||||| |||||||||||||| || || |||||||| || ||||| || || ||||
----gtatatctcttctcattctaaatttgcatatt--gttcatacaaatcggacatttgatctgattgtttctca-taaattagGTTCTTATGGACTTCCCACAATTGACAATGACGTTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------------------------------------------------------------------------gtttgtccttttc--ttctcttttcaa---tgctaata-actaggttttaacatcttgg-agatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
                                                                                           ||||| |  |   |  | ||||  |   || |||||   ||   ||| |   | ||| |  |  ||||     |   |||   | |  |||| || ||||||||||| ||  |||| |||||  | |||||||| |||||||| ||||| |||||||| || || || ||||||||||| ||||| ||||
gtgtggtcttgcctggacaattttcttgaagcatgggtttcaattttataacaatgtgtattgctgttgttaaaacttgtgcattatcaagttgtcttgctacatcatatttttgagtgtggtaatacgataatatttcatgccatggtatgtagttaactgttggagctgtggtgtgtagGTACTAATGGATTTTCCACAGCTGACAATGACCTTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------------------------------gtttgtcctt----ttcttctcttttcaatg------ctaat-aactaggttttaacatcttggagatttttaatccaggttactgaatt------attcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
                                                                   | || |       ||||||   || || ||      || || ||||     ||  | |||   |  || |  | |||  ||  |    |       |  |||| || ||||||||||| ||| ||||||||||  | || || || || || || || ||||||||||| ||||| |||||||||||||| ||||| ||||
gtttcgtaatgtgaccataacttccttgctcgtaatcaaattgttcatctttgcggatgtttacgaatctgactcagggattcttcctattgcagtggggtatctcatgaactcaaagtttgcttctccaaatttatgtaaccaatttgtttggcttgtggtgtgtagGTGCTGATGGATTTTCCACAACTGACGATGACCTTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------------------------------gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattatt-----cagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
                                                                    |||  | || ||| |   |  | ||        || |   |       | | |   | || |  |  |   ||  ||  |      |||| || ||||||||||| ||||||||||||||  ||||||| || || || || ||||| |||||||| || || || |||||||| || ||||||||||
gtgtgatattatgaccttctgggccagcaattaaattacttgagctttttggacgtttataaagctacttgcgcgtt-cttgttcgtcaagtggagtattgtatgaagtgcttctctaggggcgtatactgaacatccttgggttgctgtatgtagGTGCTCATGGATTTTCCGCAATTGACGATGACCTTGCCTGACGGACGAGAGGAGTCTGTTATGAAGCGGACCACTCTCGTGGCCAATACATCAAATATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 10
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
                          |    |  ||||  |||  ||| ||    || |||  | |     |     |  | |||||  | |  || ||||| ||  | || || ||||| |||||||| || ||||| |||||||||||||| || || || || || || |||||||||||||
--------------------------gtcggtt-ctagaatttcccatttttcttatctttgtttctacaaatcacctcttgcagGTGTTGAAAGACTTTCCACAGCTTACTATAACACTTCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGC

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 11
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
                          |    |  ||||  |||  ||| ||    || ||   || |    |     |  | |||||  | |  || ||||| ||  | || || ||||| |||||||| || ||||| |||||||||||||| || || || || || || |||||||||||||
--------------------------gtcggtt-ctagaatttcccatttttcttatcttgtttctacaa-atcacctcttgcagGTGTTGAAAGACTTTCCACAGCTTACTATAACACTCCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGC

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|110715176|gb|EE092929.1|EE092929
EST:     ACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAG                         GTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAA
genomic: ACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAGgtttgtcctt ... aattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAA
EST: gi|110707093|gb|EE083190.1|EE083190
EST:     ACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGCAATGAAATGGCGGAG                         GTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAA
genomic: ACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAGgtttgtcctt ... aattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAA
EST: gi|110692053|gb|EE070859.1|EE070859
EST:     ACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAG                         GTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAA
genomic: ACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAGgtttgtcctt ... aattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC
                       agatttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtccttttcttctcttttcaatgctaataactaggttttaacatcttggagatttttaatccaggttactgaattattcagGTTCTTATGGATTTTCCTCAATTGACGATGACACTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC