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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG

Basic information

species Vitis vinifera
transcript Vv11s0149g00130.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
                                                                       ||||||| |||       ||    ||  |  ||   ||  |||||| |  |  | ||    ||  | |||  |  | | | | || | ||||| || |||||| | |||||||| || ||||||||||| ||||| || ||||| ||||||||||||||||||||||||||| | |||||| |
----------------------------------------------------------------------gtaagctt-gtcttc----cctgcaaggattattgtgtttactcaaagt--tctgtttcctagaactaaaagacttattttccctg-tacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
                                                                               ||   |  |    |  |  || |||    |   | |  | | || |||| |   ||     |   |     |      | |||||||| |||||| | ||||||||||| ||||||||||| ||||| || || || ||||| ||||| |||||||| |||||  | || |||||
-------------------------------------------------------------------------------gtaggtctatttcaccaaattgtttg---ttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 10
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
                                                                            |  ||  ||    | ||   |||| ||    ||  || |      ||  ||| | | |      |  ||     |      | ||||| || |||||| | ||||||||||| ||||||||||| ||||| || || || ||||| ||||| |||||||| ||| |  | || |||||
---------------------------------------------------------------------------gtaggttgatttcactgaattgtttgtt---gtttacttagg----tttagttttttaaggctgtaaccatttctttttctctacagCGCGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGCGACCTGAAGACAG

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
||||||| ||    | ||  |   | |||  |       ||  ||| | ||||      |  || |  || ||    |  |||    |||   |||  |   | || || | | | ||         | ||||| |     |  |   |||      || ||||||| |||||||| |||||||| || ||||| ||||| ||||||||||||||||| ||||| |||||||| || |||||| |||| |||||
gtaagttcttaccttcctaaactgtttgtattag-----atcgcaaatttctactatactacttgttgaggta----taatcat--aagct--tgacctccatcaattttctttacaag--------tctctgattcatgttctatggtctc-----tttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
||||||| ||    | ||  |   | |||  |   |     ||||||| | ||      |  || |  || ||    |  |||    |||   |||  |   | || || |||        ||| ||  ||||| ||||  ||| |    | ||   || ||||||| || ||||| |||||||| || ||||| ||||| || |||||||||||||| |||||||||||||| || |||||| |||| || ||
gtaagttcttcccttcctaaactgtttgtattagaca----gtcaatt-tatactatactacttgttgaggta----taatcat--aagct--tgaactccatcaactttccttt------ttaagtc-tctga-ttcatgttcta----tgcaccctttagCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgatt----cagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
                                                                       || |   | ||           ||  ||| | | | ||   | ||| || ||    |  | || |   | ||     |  | ||| |     ||||| || || ||||| ||||| || || ||||||||||| |||||||||||||| ||||||||||| |||||||| |||||  | || || ||
----------------------------------------------------------------------gtatgtcctatcttcaag-----tgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG

upper sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 10
gtaagtt-tttgagattctctatcatgtgtgctgatcctaatgtcaattctctagct---ctttctttctccagataagctttgtcaatggagccgatgag---tttatttaaattccctcaaaataattag--gttatctgac-ttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
||| |   ||| | |||   |  |  ||||  | ||| |  |  |||      | ||   | |  |||    |   ||  ||| ||  |  |       |    | |||   || |   |  |||||   |   ||||   | |  | | |        ||| || |  ||| | || ||||| || |||||||| || |||||| | || ||||||||||||||||| ||||||||||| ||||||||| |  | || |||||
gtatgcaattttacatt---tgccccgtgtttttatctttctaccaaactctcacctgagcatgttttgcttactgaacgtttctcgtttcacatagcaaaccatctatggcaagtgttttgaaatatcgaaatgttaatagtcgcttacacctgtgtcctaaatca--cagAGAGAGTTTTACCTTGAAGGAGGTGCTATGGTTCTTGCTGATGGAGGTGTTGTCTGCATTGATGAGTTCGACAAAATGCGACCTGAAGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
                     atctgac  putative branch site (score: 3)
       aaaataattaggttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA