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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtattatggcaatgcatccgttaaattttctatgaggctttgttgcctcattactcagtttaattggtagttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC

Basic information

species Vitis vinifera
transcript Vv13s0019g04590.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 2
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtattatggcaatgcatccgttaaattttctatgaggctttgttgcctcattactcagtttaattggt---agttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC
                                                                    |       || ||||    |||   |||  | || | |  | || || |    |  | | |  |  |   | ||| |      |   |||||| || |||||||| ||||| || || || ||||| || ||    ||||||||||| ||||| || ||||| || || || ||||||||||||||||| || ||| |||
------------------------------------------------------------------ttggaatcagaatgatttaatttagatcaac-cttctgattgacttactctagatcaatataga-tagtgcttgagtgtggcatattcgagttttaatgcagATAAATCCTGAGAAAGCCCGAGAAGAGTTTCGTGCAGCAAGTCAGAAGAATGGAGGGACTGGGGTAAAGGACTTCATGGATGGCATGGGACTGGGAGTGC

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 2
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtattatggcaatgcatccgttaaattttctatgaggctttgttgcctcattactcagtttaattggtagttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC
                                                        || | |     |  | ||   | || ||      ||  ||||  |    || |||      || ||    |  ||| ||   | |  |   || | ||||||  | |||||||| ||||||||||| ||||| || || || |  | |||||| |||||||| ||||| || || ||||||||||||||| |||||||||||||  |||
--------------------------------------------------------ttttttagtggaaacaatagga-gagtgccccactgtgaatgtctagaatagatt------gatgcgcactgtccttatgtgtgacat--gttcggagttttggtgcagATAAATCCTGAAAAGGCCCGGGAGGAGTTTCGGACAGTAAGTCAAAAAAATGGAGGAACAGGAGTAAAAGATTTCATGGATAGCATGGGCCTTGGGGTGC

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 3
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtatta--tggcaatgcatccgttaaattttctatgaggctttgttgc-ctcattactcagtttaattggt-agttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC
    |||      | || |||||| |          |   |||  |||||  |||   |||      |    |||| | |||||| |||   ||  | |   |  ||   ||||  ||| |  | |   | | || |||      | || ||  | | ||    |||||||||||||||| ||| || ||||||| || || |||||    ||||||||||| |||||||| |||||||| ||||||||||||||||| ||||||||| 
----gtaagttggcatttctgtataa----------taaattggctgata--tttagcatcctgtttacttgatgacatgattggcattttttgagattatgtgtgtaccatttaatataatacctctctccacttatttaagtttgtagttccttacttcatttacagATAAACCCTGAGAAGTCTAGGGAAGAGTTTCGAAATGCCGCCCAGAAAAATGGTGGAACTGGAGTCAAAGACTTCATGGATGGCATGGGTCTTGGAATGA

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 3
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtattatggcaatgcatccgttaaattttctatgaggctttgttgcctcattactcagtttaattggtagtt--ttcat--acagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC
    |||      | || |||||| |     ||  |  | || ||     ||   ||| |||          |||| | |||||||||| |   |     |  ||  | | ||  ||          |  |   ||| | |  ||  | | |  ||  |||||  |||||| |||||||| |||  | ||||||| || |  |||||    |||||||| || ||||| || |||||||| ||||||||||||||||||||||||||| 
----gtaagttggcatttctgtataatagattggctgatatttagc----atccggttttcttg--------atgacatgattggtattttttgagattgtgtgtgtagtatttaatataataccactctccacttatttaagtttgtagttccttacttcatttacagATTAACCCTGAGAAGTTTAGGGAAGAGTTTCAAAATGCCGCCCAGAAAAAGGGTGGAACCGGAGTCAAAGACTTCATGGATGGCATGGGCCTTGGAATGA

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|351013747|gb|FQ433899.1|FQ433899
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|352790386|gb|FQ478026.1|FQ478026
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|294965156|gb|GW836987.1|GW836987
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|349820813|gb|FQ404198.1|FQ404198
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|349812310|gb|FQ406331.1|FQ406331
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|161720443|gb|FC070210.1|FC070210
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|26257255|gb|CA808318.1|CA808318
EST:     GGATGCTGCTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGCGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|349817149|gb|FQ405154.1|FQ405154
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAA
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAA-
EST: gi|349827879|gb|FQ422747.1|FQ422747
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|351025874|gb|FQ427886.1|FQ427886
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
EST: gi|351029701|gb|FQ427541.1|FQ427541
EST:     GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAG                         ATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT
genomic: GGATGCTGGTACCAGTTGAAGGACCTGATTCACCATTGTTTGCTCTTGAGgtatgtacag ... tttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctatgaggctttgttgcctcattactcagtttaattggtagttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC
                               gtttaat  putative branch site (score: 4)
                                            ttttcat  putative PPT
                              agtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacagaaaccttcctgtatgagtatctgctttgttttgagtgataattttgttatctcacacagcccatgaaacgattggtattatggcaatgcatccgttaaattttctatgaggctttgttgcctcattactcagtttaattggtagttttcatacagATAAACCCTGAAAAGGCTCGGGAAGAATTCCGCAATGCAAGTCAGAAAAATGGGGGAACTGGTGTCAAAGATTTCATGGATGGCATGGGCCTTGGAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA