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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatggtttaaatttcttgtctttgaatttctttcgctttattccttatttattgttagagtctgttcctaatatttattttctctctattgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAG

Basic information

species Vitis vinifera
transcript Vv15s0046g02040.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------gtcatggtttaaatttcttgtctt--tgaatttctttcgctttattccttatttatt-gttagagtctgttcctaa---tatttatttt----------ctctctattgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAG
                                                       ||||| |  |  |      ||  |||| | |    |  |  |  |||||  ||| | ||   |||  |||  |   |||||||| |          || |  | | ||  |||||||| |||||| | ||| ||||||||||| ||||||| |||  | ||||||| |||||||| || || || |||||||| || ||  | |||||||||
gtatgtttgtgttctcaattttagcacctcagttattatatgttttaacatttgaatggtgttcacctgcaagattagtgaagtacaaaagtatcttggcttatgaatttgctatgttctaatccccaacatatttattctgaacctctagctttggacttttttcagCAAACTATTTGGCTCTTCATTAGGGACATGATCAAAGGGATTTTGCTATCCATCTTACTTGGACCTCCTATTGTGGCTGCTATTATCATCATAGTACAG

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------gtcatggtttaaatt----tcttgtctttgaatttct--ttcgctttattccttatttattgttagagtctgttcctaatat--ttat-tttctctctattgtt-cacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAG
                                                                  |  | |||| | ||    |||  | |||| | |  |  |  | |||  |  |     |||  || | |    ||||| |||  |||| ||| | |||  | ||  ||||||||||   ||||||||||||||||||||| | |||||||||    | ||  |  || |||| ||||| || ||||||||||||||||| |||||||||
gttcatattcttccatcaaattcaaccatctatctgttatttcatccatgtttttagttcacaccattttagtttgatttgacatctcatttttgtaatattgataagttttgctgttgtaaaattcgtatatttgtgtcctactatccttatgtttttatcttctattatacagCAAACACCATGGTTATTCTTTAGGGACATGCTTAAAGGAATTTTCCTTTCTGTAATAATTGGTCCACCTATTGTGGCTGCAATCATTGTAATAGTACAG

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 5
gtcatggtttaaatttcttgtctttgaatttctttcgctttattccttatttattgttagagtctgttcctaatatttattttctctctattgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAG
             | | | || |||  |   ||  |   | | |     ||| || | ||||  |||   | | ||||  || ||   |  |||| |||||||||||| ||| | ||| ||||||||||| |||||||||      | ||  |  |||| || |||||||| || ||||| || ||| | ||||| |||
------------gtatgtcgtatttccaacactaccttgtgacttacgtttttttatcagaga-tgtggattaaatttgctt-ctaaattctgttgacagCAAACAATATGGATGTTCATTAGGGACATGATCAAAGGAACATTCCTCTCTGTCATACTAGGCCCACCCATTGTTGCTGCGATAATTTTCATAGTCCAG

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|349814570|gb|FQ399210.1|FQ399210
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|30304044|gb|CB980838.1|CB980838
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGAACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351052220|gb|FQ452374.1|FQ452374
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351043081|gb|FQ451254.1|FQ451254
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|110700064|gb|EE077676.1|EE077676
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351012828|gb|FQ430391.1|FQ430391
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351045038|gb|FQ449292.1|FQ449292
EST:     TTTCTCTATACTCAACCTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|30304107|gb|CB980901.1|CB980901
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGAACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351040629|gb|FQ438173.1|FQ438173
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351033796|gb|FQ447834.1|FQ447834
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATCCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|349820667|gb|FQ408496.1|FQ408496
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351044625|gb|FQ443156.1|FQ443156
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351043828|gb|FQ452622.1|FQ452622
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
EST: gi|351029807|gb|FQ427647.1|FQ427647
EST:     TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAA                         CAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC
genomic: TTTCTCTATACTCAACTTTTGTGATTGAGGCCCGCCATGGTTTCAACAAAgtttgtattc ... ttgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatttattgttagagtctgttcctaatatttattttctctctattgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAG
                      tcctaat  putative branch site (score: 2)
                              tttattttctctctat  CT-rich tract
                         taatatttattttctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatggtttaaatttcttgtctttgaatttctttcgctttattccttatttattgttagagtctgttcctaatatttattttctctctattgttcacagCAAACAATTTGGTTATTCTTTAGGGACATGTTCAAAGGAATTGGGTTATCCATTTTACTTGGGCCACCCATCGTGGCTGCAATCATTGTTATAGTACAG

- catggtt