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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT

Basic information

species Vitis vinifera
transcript Vv13s0156g00180.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT
                          |    |||| || |||     | |   | |||  | | ||||   ||    |  |        ||||| |  | ||       |||   | |  ||| | || |||||||||||||||||  |||| || || || || || ||||| || ||||| ||||| ||||||||||||||||| || || || | |  ||
-------------------------gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaat--------tctgacttgtgata-----cattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 19
---gttctcactatgt-ccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT
     ||||||| |   |  ||  | || ||||| |    | | || | |||||||          | |     | |||||| |||     || |  | || ||   |||||       | || ||| | || |||||||||||||||||  |||| || || || || || ||||| || ||||| ||||| || |||||||||||||| |  || || | |  ||
gtatctctcactttccactttctacctcatttctttggatcttctctgcattttgtactacaatgcagaggatcc-ttcttcattctat--caaccaattctttcacattatc----tgtgtcgcagCTCATTTGGGACCGTGCTCTTGGCCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAGAACCACTGCAAGAAGGTTGCTGCTTGAAGCT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G063851_T01 (Zea mays), 3'ss of exon 20
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctc---attcttccttcg-ggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT
                                                  || ||  ||||    |||||    ||  || ||| |   | |  |||  | ||| |  ||  |  ||  |    ||| | || ||||||||||| |||||  |||| ||||||||||| || |||||||| ||||| ||||| || ||| ||||||||||    || || | |  ||
--------------------------------------------------gtctgccttctaccttctcttgatatagtttcttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCTTGAAGCT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctg--aatcattattatt--attatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT
                             | ||||  | |  |  |  | ||| |   |||  ||     ||  |   |     ||   ||||      | | || ||  ||||||| |  |  ||| | || ||||||||||| |||||  |||| ||||||||||| || |||||||| ||||| ||||| || ||| ||||||| ||    || |||| |   |
--------------------------caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattttgtttgattatttatgatg-cagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT
                         | |  ||||| ||||  |    ||||     ||||| |      | ||||| ||  |   |     |   | ||| | ||||| ||         ||| | || ||||||||||| |||||  |||| || |||||||| || || ||||| ||||| ||||| || ||| ||||||||||    || |||| |  ||
------------------------gtctgccttctaccttctc----tttgcacagtttctaag-----taattctgccggctaattttgtttggttatt-taattatgatg--------cagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 19
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttctta---aatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGC---AGCCGCCTAATTCT
                         |  |   | |   ||| |  |||  |  | | ||  ||   ||  | | |  |     ||   ||| |||    |||| | |||  | |||  || | ||| | ||||||||||| ||||||||| |  | |||||||||||||| |||||||| ||||| |||||||||  ||| || ||||||||   | | || |||    
------------------------gtaacatatatatatttacacattacgcctttgttactacataacatttaaaacagaactcatatgc-tct---ccattctcatttgtgtttaatt-cacagCTTATATGGGACCGAGCTCTTGGACTTGCACTTGAGAGGCCAAAGAGTGTTACCATGGACTGGCTTGAAGCCCATTGTAAGAAAGCTTCATCTGCTTAAG---

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|34544605|gb|CF512837.1|CF512837
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|34319605|gb|CF372359.1|CF372359
EST:     ATTTTGCTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGTCCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110391493|gb|EC956472.1|EC956472
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110418511|gb|EC984670.1|EC984670
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110361418|gb|EC924886.1|EC924886
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110429398|gb|EC995889.1|EC995889
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110367719|gb|EC931670.1|EC931670
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|34320089|gb|CF372843.1|CF372843
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|34363396|gb|CF404981.1|CF404981
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|34415969|gb|CF414723.1|CF414723
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|29785895|gb|CB343236.2|CB343236
EST:     ATTTTACTGTTCTTTTCGGGGTATCGAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|71866113|gb|DT015168.1|DT015168
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110372355|gb|EC936513.1|EC936513
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|71866222|gb|DT015277.1|DT015277
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|34546327|gb|CF514559.1|CF514559
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|110362967|gb|EC926531.1|EC926531
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTT
EST: gi|77577886|gb|DV217693.1|DV217693
EST:     ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAG                         TTAATATGGGACCGTGCT
genomic: ATTTTACTGTTCTTTTCGGGGTATCAAGGAGTATAGGGATCTGCTCTCAGgttctcacta ... cttttctcagTTAATATGGGACCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT
                                    ttattatttcttttct  CT-rich tract
                    atctgaatcattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA