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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgtatttgttatgaatgacaaacttgacactttttcttacgattctagtcatattgatccctatatgttttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTA

Basic information

species Vitis vinifera
transcript Vv07s0005g02820.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------------------gtatcttgtatttgttatgaatg---acaaacttgacactttttcttacgattctagtcatattgatccctatatgttttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTA
                                                                                               |  ||    ||   |  | |     ||  |||||| |   |   || |          |  ||    | ||| ||||| |||||||||||| ||||||||||| ||||| ||  | ||||||||||||||| ||||||||  ||||||||||||||| |||||  | ||||| |||| ||| ||  
gtaagtgaaatttcttattgaagcaattttgaacttcctcttgctttattgtgtgtggttttgaacattcataatcacgacaaacttttagtcttttcctccctttctctccggacacacacctacttgagagactggattccttaaaggaagaatttatatcttatctgtttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGTTGTGATGGGGGATATCCCTTGTATGCGTGGCAATACTTAG

upper sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------------------------------------------------gtatcttgtatttgttatgaatg---acaaacttgacactt-------tttcttacg-attctagtcatattgatccctatatgttttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTA
                                                                                                 | |||    ||   | || |     ||  |||||| ||||       |   ||||       |   || ||    | ||| ||||| |||||||||||| ||||||||||| ||||| ||  | ||||||||||||||| ||||||||  ||| |||||||| || |||||  | |||||||||||||| ||  
gtaagtgaaatttcttattgaatcaattttgaactacatcttgctgtattgtgtgtgattttgaatattcacgatgatgataattttttagtctttttctctccctttctctctggacacacacctacttgagacttgagagactggattacttgaaggaagaattttatatcttatctgtttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGCTGTGATGGAGGATATCCCTTATATGCATGGCGATACTTAG
















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|110717706|gb|EE093795.1|EE093795
EST:     TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|110375663|gb|EC940672.1|EC940672
EST:     TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|110731310|gb|EE105611.1|EE105611
EST:     TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|351041020|gb|FQ443796.1|FQ443796
EST:     TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|110420331|gb|EC986603.1|EC986603
EST:     TTGGTGCTGTTGAATCGCTGTCGGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|110406274|gb|EC971841.1|EC971841
EST:     TTGGTGCTGTTGAATCGCTGTCGGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|351027477|gb|FQ444726.1|FQ444726
EST:     TATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: TATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
EST: gi|110360706|gb|EC924023.1|EC924023
EST:     GAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG                         AATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT
genomic: GAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATGgtatcttgta ... tttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacactttttcttacgattctagtcatattgatccctatatgttttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTA
                                            ttttatt  CT-rich tract
                                      tatatgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttgtatttgttatgaatgacaaacttgacactttttcttacgattctagtcatattgatccctatatgttttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG