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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattagccgtggttaatattctaatttgtccatcaaaaaatggtgggggtaaaacatgagttgttactcatcagtttgcttgtattgagtttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAATGAGGTATCTCCGTCATGTTCCATGTAGGTTTAAGAGTAACTTCAGAGA

Basic information

species Vitis vinifera
transcript Vv04s0008g03900.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g56990.1 (Oryza sativa), 3'ss of exon 2
-tattagccgtggttaatattctaatttgtccatcaaaaaatggtgggggtaaaacatgagttgttactcatcagtttgcttgtattgagtttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAATGAGGTATCTCCGTCATGTTCCATGTAGGTTTAAGAGTAACTTCAGAGA
    | || ||  | | |  |  | ||||              |      | | |  | |||| | |||  |  | ||  || |    | ||  ||   ||| || |||||||||||||| ||| | ||||||||||||||||| ||| | |||||||| || || || || ||    ||||| |||||||||||||||||
tctcttgctgttttcattgatgaagtttgatagaatctgctcagctcctctgatatgt-agttctgactactttgattctttctcgaaatttgaaacacagACAACTGGAGTGTGAAGGCCATCAGGAGGAAGACCACTGGAACTGGGAGGATGAGGTACCTTCGCCACGTGCCCAAGAGGTTCAAGAGTAACTTCAGAGA

upper sequence: Vv04s0008g03900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ06862 (Selaginella moellendorffii), 3'ss of exon 1
tattagccgtggttaatattctaatttgtccatcaaaaaatggtgggggtaaaacatgagttgttactcatcagtttgcttgtattgagtttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAATGAGGTATCTCCGTCATGTTCCATGTAGGTTTAAGAGTAACTTCAGAGA
        |||   |   ||||  |   |   ||      ||||||     |  |  |||      ||||  |  |  || | | |    | |  | ||||||| ||||| | |||||| |||||  | |||||||||||||| ||||| |||||||| || || ||| | ||  |  | || ||||| |||||||||||
--------gtgagaagagttcttctcccttgttct-----tggtgg-----atccgcgag------ctcacgaaat--ctcgaaatct-ctcgtgtgtagATAACTGGAGCGAGAAGGCGATCCGGCGCAAGACCACTGGAACCGGGCGGATGAGGTACCTGCGCCATCTCCCCAGGCGATTCAAGAGCAACTTCAGAGA

upper sequence: Vv04s0008g03900.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ34847 (Selaginella moellendorffii), 3'ss of exon 1
tattagccgtggttaatattctaatttgtccatcaaaaaatggtgggggtaaaacatgagttgttactcatcagtttgcttg-tattgag----tttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAATGAGGTATCTCCGTCATGTTCCATGTAGGTTTAAGAGTAACTTCAGAGA
                                          ||| ||  |   |     |    |  |   || |  |    | | ||      | |  | ||||||| ||||| | |||||| |||||  | |||||||||||||| ||||| |||||||| || || ||| | ||  |  | || ||||| |||||||||||
------------------------------------------gtgaggagacttctcccttgtggatccgcgagctcacgaaatctcgaaatctctcgtgtgtagATAACTGGAGCGAGAAGGCGATCCGGCGCAAGACCACTGGAACCGGGCGGATGAGGTACCTGCGCCATCTCCCCAGGCGATTCAAGAGCAACTTCAGAGA

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|110716567|gb|EE091662.1|EE091662
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110426007|gb|EC992404.1|EC992404
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110428159|gb|EC994622.1|EC994622
EST:     CGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: CGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110692276|gb|EE071338.1|EE071338
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110705824|gb|EE083118.1|EE083118
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|34321111|gb|CF373865.1|CF373865
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110393500|gb|EC958783.1|EC958783
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110693836|gb|EE070416.1|EE070416
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110392473|gb|EC957921.1|EC957921
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110707741|gb|EE084486.1|EE084486
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|71870115|gb|DT019170.1|DT019170
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|71868943|gb|DT017998.1|DT017998
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110388252|gb|EC952984.1|EC952984
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110409567|gb|EC975233.1|EC975233
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|30301004|gb|CB977798.1|CB977798
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110717458|gb|EE093330.1|EE093330
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|71869027|gb|DT018082.1|DT018082
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|71868495|gb|DT017550.1|DT017550
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110424590|gb|EC990957.1|EC990957
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110707148|gb|EE083294.1|EE083294
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110695260|gb|EE073077.1|EE073077
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|34415393|gb|CF414147.1|CF414147
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110386000|gb|EC950569.1|EC950569
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110409906|gb|EC975580.1|EC975580
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
EST: gi|110401323|gb|EC967930.1|EC967930
EST:     GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAAT                         ATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA
genomic: GAAGAGCCGATGCGCTGCTTGTGGATTTCCTTCTAGCCGGATCCGAAAATgtgagtcatt ... ttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggtaaaacatgagttgttactcatcagtttgcttgtattgagtttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAATGAGGTATCTCCGTCATGTTCCATGTAGGTTTAAGAGTAACTTCAGAGA
                                            tttgaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattagccgtggttaatattctaatttgtccatcaaaaaatggtgggggtaaaacatgagttgttactcatcagtttgcttgtattgagtttgaatttagATAATTGGAGTGTGAAGGCAATCCGCAGGAAGACCACTGGAACAGGGCGAATGAGGTATCTCCGTCATGTTCCATGTAGGTTTAAGAGTAACTTCAGAGA

- - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - -ggtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - catgagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcatc