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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA

Basic information

species Vitis vinifera
transcript Vv05s0020g04210.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G088348_T01 (Zea mays), 3'ss of exon 9
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgta-attgccttaccttca-gttctaattctgat-------taatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                                    |||    || | |  || |     ||  |    ||  ||  | |    ||  |||| ||||| |||||  |       ||| | ||   || |     |||| ||||| || || || ||  | |||||  ||||||| ||| | ||||| || ||||| ||||| |||||||| ||||||||||||||||||||||| |
------------------------------------gaatgatagctttttctgtaatgaaacaggtggtttggtggactatactatgttcaagttctgattcttgtactgttctaacactgttgatttctactagGTTCTTGAGGAAGGCGTCCTCAACCCAGAATCAACTGTTGTTGCGATTTTTCCCTCTCCAATGCATTATGCTGGGCCAACTGAGGTGCAGTGGCATGCTA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G302080_T01 (Zea mays), 3'ss of exon 9
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgat-taatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA---------
                                 |||     || || ||    | |   |   |||  | |||   || |    |  |    ||||  | ||| | ||| | ||   || |     | || ||||| || || || ||  | |||||  ||||||| ||| | || || || ||||| ||||| |||||||| ||||||||||||||||||||||| |         
--------------------------------ctttt----tctgtaatgaaacaggtggtttggtggactatactat-gttcaagttctgattcttgtactgttctaacactgttgatttctactatgttcttgagGAAGGCGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTTCCCTCTCCAATGCATTATGCTGGGCCAACTGAGGTGCAGTGGCATGCTAAGGCTCGTA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 3
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgat-taatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                       || |      |||      | || ||    | |   |   | |  |||||   || |    |  |    ||||  | ||| | ||| | ||   || |     |||| ||||| || || || ||  | |||||  ||||||| ||| | || || || ||||| ||||| |||||||| ||||||||||||||||||||||| |
----------------------ataatagctttttt-----cctgtaatgaaacaggtggtttgatggattatactat-gttcaagttctgattcttgtactgttctaacactgttgatttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTTCCCTCTCCAATGCATTATGCTGGGCCAACTGAGGTGCAGTGGCATGCTA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G149952_T01 (Zea mays), 3'ss of exon 2
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaaggg-----tccattatgtaattgccttaccttcagttctaattctgat-taatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                                  ||||      | ||| ||| |     ||  |     |  ||      | | |  ||  ||||  |    | ||| | ||| | ||   || |    ||||| ||||| || || || ||  | |||||  ||||||| ||| | || ||||| ||||| ||||| |||||||| ||||||||||| || |||||||| |
---------------------------------attgagtgatggctattcctgtaatgaaataggtgttttgatggcaccactacactatgttcaacttctgtactgttctaacactgttgatttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 2
gttcatgaactgatcctatgatgtattgctcaatttgaaaat-cagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                       | |  ||||  |     || | ||  |  || || |       |  |  || | |||   | | |   |   || | |   || ||| | |      ||| | |||| ||||| ||||| ||||||||||||||||||||||| || || || |||||||||||||||||||||||||| || || |||||||||||||||||||
-----------------------tctccctcacctaagttattctgtggtttctttgtctccctaatt-agcat-tgatttgttcaacagaaaaactcacttgtatcaatttggt---ctttctttagGTACTTGAGGATGGTGTTCTTGATCCAGAGACAACTGTGGTATCCATATTCCCATCTCCCATGCACTATGCTGGACCCACGGAGGTGCAGTGGCATGCAA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 2
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                      |  |  |||  ||  ||  |  ||  |  |  || |      ||  || || | |||   | | | | |   ||   |   || ||| | |      ||| | |||| ||||| ||||| ||||||||||||||||| ||||| || || || ||||| |||||||||||||||||||| || || |||||||||||||||||||
----------------------gcctgtctcccttctaatttatgtagtttcattgtctccctagtt-atcat-tgatttgttcaacataaaaactcccttgtatcaatttggt---ctttctttagGTACTTGAGGATGGTGTTCTTGATCCAGAGACCACTGTGGTATCCATATTCCCTTCTCCCATGCACTATGCTGGACCCACGGAGGTGCAGTGGCATGCAA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G14680.1 (Arabidopsis thaliana), 3'ss of exon 2
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                      |||||     | |  ||      || | | | |         || ||||||   |               | || |     |||  | || |  |  ||  | ||||||| || ||||| ||||||||||||||||| ||||| ||||| || ||||||||||| |||| ||||||||||||||| || || || ||||| ||||
----------------------gtattaacggaatcaaagtctttttttgcgtgttgtttgctagttcattatagga-------------gatgctga-----attggttttcatgac-ttgattagGTGCTAGAGGATGGTGTTCTTGATCCAGAGACTACTGTGGTTTCCATATTCCCATCTCCAATGCTCTATGCTGGTCCAACCGAAGTCCAATGGCACGCAA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------gttcatgaactgatcctatg-atgtattgctcaatttgaaaatcagttatccctctgccagaagg-gtccattatgtaattgccttac----cttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                       | || |||  | | || || ||  |  |   | ||   |      |||    |     |   |   |   || |  | |  |  ||         |  | | ||  || |   | ||||           ||||| | || ||||| || || ||||||||||| |||||||| ||||| ||||||||||| ||||  || ||||| ||||||||||| || |||||||| |
gtatctctttcactttcttctcttccaagaaacgttactttggatacaaagtgtatttcagatgagctttagattttgatgaattgatattggttgttgattctcgctatggagtgaaaaatgttatattgttgtttcttgatttgaacatgtagGTGTTGGAGGATGGTGTACTGGATCCAGAGACCACTGTAGTCTCTATCTTCCCATCTCCGATGCTATACGCTGGCCCAACTGAGGTTCAATGGCATGCCA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 2
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgcct-taccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                                     ||||  ||||||   | ||      |  ||     ||| | ||  | || ||| |     ||| || | |    ||   |||||    ||||| || || ||||| ||||| ||||| ||||| || || ||||| || ||||| || || ||||| || ||||||||||| || ||||||||||| ||||
-----------------------------------gtaaaaaaagttattgat-tgttgtgtgtctcttgagtgtgagtgtgtgtatcttga-----aatgctaaatgtgtttatgaatgtaaaacagGTTCTAGAGGATGGTGTTCTCGATCCGGAGACTACAGTGGTTTCGATATTCCCGTCACCTATGCATTACGCTGGTCCAACCGAAGTGCAGTGGCACGCAA

upper sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S331_37V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------gttcatgaactgatcctatgatgtat-tgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgatt-aatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                                              || |||   |||| ||| |||  | || ||  |    |  |  || |    |    || ||    ||   | |  | ||     |          |||   | ||  |  ||| ||   ||    |||| |||||||  || || ||||| || | ||| || || ||  | |||||||| |||||||||||||| || || || || |||||||| |||||||| |
gtatcgtacctttaccagctctcctggccaattaactttttcgcagtc-tgagtagatcatattatgcgtctgatcggtaccgag-tttgtgagttttaaatcataata--cccccacgacaatgttgagcaagagaaaagaatatcgttttgacgttgcaacaattttgtagGTCCTTGAAGCCGGAGTCCTTGACCCTGCGACCACCGTTGTGGCCATTTTCCCCTCTCCCATGCACTACGCCGGACCGACGGAGGTGCAATGGCATGCTA

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|161714062|gb|FC063798.1|FC063798
EST:     CAAAGGCAGATGATGTTCCGCTTGGTTGGAGAATGAAGCAACATGAGAAG                         GTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTC
genomic: CAAAGGCAGATGATGTTCCGCTTGGTTGGAGAATGAAGCAACATGAGAAGgttcatgaac ... tgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA
                                             tgttcctc  CT-rich tract
                       taattctgattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagGTGCTTGAAGATGGGGTTCTTGATCCAGAGACAACTGTAGTTTCTATTTTCCCATCTCCCATGCACTATGCTGGTCCAACTGAGGTGCAGTGGCATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG