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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaattattctcttagccactccactgcataaatgatatgatattcggaaaggcatactgagaaaaaaaattccttttcttccatgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCAAAAGCAAAATCCAAAGGGCTGAAGAATGCAAAGAGATGGAATTGAGTGA

Basic information

species Vitis vinifera
transcript Vv07s0031g01640.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G39670.1 (Glycine max), 3'ss of exon 8
--------gtaagaattattctcttagccactccactgcataaatgatatgatattcggaaaggcatactgagaaaaaaaattccttttcttccatg---------actaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCAAAAGCAAAATCCAAAGGGCTGAAGAATGCAAAGAGATGGAATTGAGTGA
         |   | |||    | |      ||||  |   | |  | |   ||||    ||     |  |||     |||||| |||  |||  |          | |||||||||||||| || ||   ||||||||| || | |||||| |||||||| ||||||   || ||||||||  |||| ||||| |||||||||||||||||||
gtaaacttttgttagttaaatccatgagatgtccaaggttaacactaaacagtattgcataatttccagggagcttgtaaattcgtttctttctttctgtttttgcaataacagGCTGAGAAAGAGGCACGGAAGAAACAAAAGATGCAGGCCTTTCAGGCAGCAAAACAGAAGTCCAAAGGCGTGAAAAATGCCAAGAGATGGAATTGAGTGA

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G15200.1 (Glycine max), 3'ss of exon 8
--------------gtaagaattattctcttagccactccactgca-taaatgatatgatat----tcggaaaggcatactgagaaaaaaaattcctt-------ttcttccatg-actaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCAAAAGCAAAATCCAAAGGGCTGAAGAATGCAAAGAGATGGAATTGAGTGA
              ||   |   ||    |  |    |  |   || | ||   |||   ||    ||      |  | || | |||     ||| ||       || ||   || | |||||||||||||| |||||   ||||||||| || | |||||| |||||||| ||||||   || || |||||  |||| ||||| |||||||||||||||||||
gtaaacttttgttagttgaacccatgagatggggtggttaataacacttaacagtattgcataacttccagggagggtgcttataaattcgtttctttctaattttttttttttgtaataacagGCTGAGAAAGAAGCACGGAAGAAACAAAAGATGCAGGCCTTTCAGGCAGCAAAACAGAAGTCTAAAGGCGTGAAAAATGCGAAGAGATGGAATTGAGTGA
















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|37190151|gb|CF609500.1|CF609500
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|110391761|gb|EC956761.1|EC956761
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|56409612|gb|CX017864.1|CX017864
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|352772399|gb|FQ469924.1|FQ469924
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|26261553|gb|CA812616.1|CA812616
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|27755077|gb|CB035832.1|CB035832
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|30301899|gb|CB978693.1|CB978693
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGATCC-GATCNAGGCAGGCATTTCAGGCTGC
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAA-AGGCAGGCATTTCAGGCTGC
EST: gi|32248178|gb|CD713997.1|CD713997
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
EST: gi|30135054|gb|CB920392.1|CB920392
EST:     AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAG                         GCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA
genomic: AGCTTGATGAGAAGGCCCCTAAAGTAAAAGCCAAATCCAAGATGTCAAAGgtaagaatta ... tgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattcggaaaggcatactgagaaaaaaaattccttttcttccatgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCAAAAGCAAAATCCAAAGGGCTGAAGAATGCAAAGAGATGGAATTGAGTGA
                               ttccttttcttccat  CT-rich tract
                       aaaaaaaattcctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaattattctcttagccactccactgcataaatgatatgatattcggaaaggcatactgagaaaaaaaattccttttcttccatgactaacagGCTGAGAAGGAAGCCATGAAGAAACAGAAAAGGCAGGCATTTCAGGCTGCAAAAGCAAAATCCAAAGGGCTGAAGAATGCAAAGAGATGGAATTGAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA