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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag

Basic information

species Vitis vinifera
transcript Vv19s0015g01950.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 5'ss of exon 5
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag
|| ||||| ||||| ||||| || |||||||||||||| ||||| |||||||||||||| || ||||| || ||||||||| ||   |  |||  | ||||| ||  ||||||     |    | || | |     | ||||   |  || |  | || |    || ||     ||| || ||  |||                                                         
ACTGTAGAGGCAGAGAGGATATCTGTTGATCATGTTGCCCATCTCAAACCATCTGATGGTGGCTCTGCGGCGACTCAATgtgagggttcttctt-atcatcagtttatgtcttacagatattgagttgtactacccaatata--ttgtttttggaaaaatg---atactgacagatatat-ttgagcag--------------------------------------------------------

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G028089_T01 (Zea mays), 5'ss of exon 5
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag
|| ||||| || || ||||| || || || |||||||| ||||| |||||||||||||| ||||| || |||||||| |||||||  |     | ||     |||   | | | ||||  | ||  |||   |    | |     |   |   | |  | |||   | || |||| | ||| |    ||| |   | | |     | || || || |   |  |      | |   |||||||||
ACTGTAGAGGCTGAGAGGATATCTGTGGACCATGTTGCCCATCTCAAACCATCTGATGGTGGTTCAGCAGCAACTCAGTgtaagcatt-----ctac-----tttgaagccctctctcaaaacaaatttatggg---tcagtgggtgtcttccccgtggctttg--ctttctcaacaaatagt-catattatccgaggtat----ttttctggatagaaatgtactaaacgatgcttttgtgcag

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G47850.1 (Glycine max), 5'ss of exon 5
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag
|| || ||||||||| |||| |||||||||||||||||||||||||| ||||||||||| ||||| ||||| || |||||| ||   || |||  ||  |  |||    | || ||| | |  |    |   ||       ||  |  || ||     ||| ||||  | ||   ||  |||                                                               
ACTGTTGAAGCAGAACGGATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtgagtgtttttctagactcttctttgcattattatctttcattaagcctttggagtgggggaagttt-ttttatttctgttcttat--tgttaggtaattat---------------------------------------------------------------

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G12890.1 (Glycine max), 5'ss of exon 5
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag
|| || ||||||||| | || |||||||||||||||||||||||||| ||||||||||| ||||| ||||| || |||||||||   || |||  ||  |  |||    |  | ||| |||  || |||    ||   | |  | |||       ||||| |||    | |    |   | | | |                                                           
ACTGTTGAAGCAGAACGAATATCAGTTGATCATGTTGCTCATCTTAAGCCATCTGATGGTGGTTCAGCTGCTACACAATgtaagtgtttttctagactcttctttgc-attatatct-ttattatctttcattaagcctttggagtagg-----ggaagtgtttgatttctgttctgattgtcagg-----------------------------------------------------------

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G26430.1 (Arabidopsis thaliana), 5'ss of exon 5
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttt----tgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag
|| || ||||| ||||| || || |||||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||  |  | ||       |||| |  |  | | |  |  | ||||    ||||   |||| ||   |  |||  |      |||| | |                                                                             
ACAGTTGAAGCTGAAAGAATATCTGTTGATCATGTTGCACATCTTAAGCCATCTGATGGAGGCTCAGCTGCGACTCAGTgtaagctttattatcacttcatatttatcataatctgttctttctttttcatctgcatggaattttaggttgattcctcga----ttttgtgcag---------------------------------------------------------------------------

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 5'ss of exon 5
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagccct-tatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag
|| || ||||| ||| |||| ||||||||||||||||| ||||||||||||||||| ||||| || || ||||| || ||| |||| | | || | |  | ||| || |        || |   | | || | |    |     | || |  | || | |                                                                                      
ACAGTTGAAGCTGAACGGATATCAGTTGATCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGTgtgagccttatgtcactaata-catatcatactccacttcctg--agtcttactgtttttggctgattattcgttcatatgcag-----------------------------------------------------------------------------------

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|110713432|gb|EE089350.1|EE089350
EST:     TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT                         TGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
genomic: TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagccctt ... gtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
EST: gi|110363635|gb|EC927237.1|EC927237
EST:     TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT                         TGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
genomic: TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagccctt ... gtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
EST: gi|110368023|gb|EC931983.1|EC931983
EST:     TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT                         TGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
genomic: TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagccctt ... gtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
EST: gi|110684768|gb|EE062427.1|EE062427
EST:     TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAAT                         TGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA
genomic: TCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagccctt ... gtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGTAGAAGCAGAAAGGATCTCAGTTGATCATGTTGCTCATCTTAAACCATCTGATGGAGGTTCTGCTGCAACTCAATgtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC