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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaaccaacaaccatctctttctcctccatggggacccaaaaaattgttgtagttgttccatctgttgactataattaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG

Basic information

species Vitis vinifera
transcript Vv18s0122g00550.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G39760.1 (Glycine max), 3'ss of exon 1
gtatgaaccaacaaccatctctttctcctccatggggacccaaaaaattgttgtagttgttccatctgttgactataattaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG
            ||   | ||| |||  |||||    |  |||          || | | | | ||| |||   ||  ||  |     | | |||   |||||||||||||||||||  | ||||| || |||||||||||||| ||||||||| | ||||||||
----------gtaattctttctatctg-tccatctatattcaa----------tattcgcttcttct-ttgttcatcttttttt---gtcaatttggttgcagAGCTTGATGTACCAGCTTTGCAAGGGCGTTGCTTTCTGCCACGGTCATGGGATCTTGCACAG

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G07640.1 (Glycine max), 3'ss of exon 2
gtatgaaccaacaaccatctctttctcctccatggggacccaaaaaattgttgt--agttgttccatctgttgactata-attaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG
                                  |  |   |  | ||   | |  | ||  |  || |||| | | |  ||| |      | | |||   | |||||||||||||||||  | ||||| ||  ||||||||||||| ||||||||| | ||||||||
----------------------------------gtaatatattatatctctctcaattttgtgaatttgttcaatgttcattcaattttgtgaatttggttacagAGCTTGATGTACCAGCTTTGCAAGGGGATTGCTTTCTGCCACGGTCATGGGATCTTGCACAG

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G08250.2 (Glycine max), 3'ss of exon 1
---gtatgaac-caacaaccatctctttctcctccatggggacccaaaaaattgttgtagttgttccatctgttgactata-attaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG
    ||  |    |   |  || |||  |  ||| ||     |   | | |||    |  ||||   || |||| | |||  ||| ||     | | |||   |||||||||||||||| ||  | ||||| ||  ||||||||||||| ||||||||| | ||||||||
gtaatactagtatatttatgatttctcacaactctatctattctatatacatt-caattcttgtga-atttgttcaatattcattcatttttgtgaatttggttgcagAGCTTGATGTATCAGCTTTGCAAGGGGATTGCTTTCTGCCACGGTCATGGGATCTTGCACAG

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G76540.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgaaccaacaaccatctctttctcctccatggggacccaaaaaattgttgtagttgttccatctgttgactataattaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG
            ||||| ||  ||    ||          |         ||||  |   |  | |     |  ||||  | |   || | || ||  |||||||||||||||| ||| ||||||||||| | || |||||||||||||| ||| ||||||||||
------gtttttaaccaccttattactgtcatctctctttctcgcttcatttgtgctcacttgaacca---aacataac-attctgaaaagttatt--tgcagAGCTTGATGTATCAACTATGCAAAGGTATGGCATTCTGCCATGGTCACGGGATATTGCACAG

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgaaccaacaaccatctctttctcctccatggggacccaaaaaattgttgtagttgttccatctgttga----ctataa-ttaatacaaata-atttttaa--tgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG
                      ||    |   ||| ||          || | |  || |  |||| | | |    || |||  ||| | ||| |  || || |  ||||| ||||||||||||| |||||||||||  | ||||| |||||||||||||| || ||||||||
---------------------gtttggatatttggagattttgtt--ctgctttttttctctcatccgataagcccctttaagctaagagaaacatgttcttgaattgcagTGCTTGATGTACCAGTTATGCAAAGGCATGGCTTTTTGCCATGGTCATGGAGTGTTGCACAG

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|34542681|gb|CF510913.1|CF510913
EST:     CAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: CAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|351046614|gb|FQ453230.1|FQ453230
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|351055531|gb|FQ442327.1|FQ442327
EST:     CCGAAGCTTCCGCCAAACTGCGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: CCGAAGCTTCCGCCAAACTG-GGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|351056035|gb|FQ453496.1|FQ453496
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|110376059|gb|EC941099.1|EC941099
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|110426132|gb|EC992529.1|EC992529
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|351039035|gb|FQ457710.1|FQ457710
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|349827747|gb|FQ422615.1|FQ422615
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|33404794|gb|CF210421.1|CF210421
EST:     CCGAAGCTTCCGCCAAACTGGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: CCGAAGCTTCCGCCAAACT-GGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|352795715|gb|FQ480303.1|FQ480303
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
EST: gi|34542594|gb|CF510826.1|CF510826
EST:     TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAG                         AGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG
genomic: TCCGAAGCTTCCGCCAAACTGGGGAGAATATTCCCACAAAAACCATTAAGgtatgaacca ... tttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtagttgttccatctgttgactataattaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG
                                            ttttaat  putative branch site (score: 3)
                                           ttttt  CT-rich tract
               atctgttgactataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaccaacaaccatctctttctcctccatggggacccaaaaaattgttgtagttgttccatctgttgactataattaatacaaataatttttaatgcagAGCTTGATGTACCAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG