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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaaactttttcacatacatgatgctattttctggaagtaatttattttgtgtttcttactatctgaacaaagttaataattcttcttgtttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT

Basic information

species Vitis vinifera
transcript Vv18s0041g01360.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 8
cgaaactttttcacatacatgatgctattttctggaagtaatttattttgtgtttcttactatctgaacaaagttaataattcttcttgtttct----ttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
    | || ||   | || ||     ||      ||| |||   |  |    |||   | || || |  |   | ||   | ||  ||  |||     || ||||||||| ||||||||||||||||||||   | | ||||| |
--tcagttcttgtaaaacgtggaataataactgtgaattaag--agctcacattttgaagtacctaagaattttgaaggttgctaatttcttcaagtgttgcagCTATTTGCCTGAGGAGATGAGGAACCCTGATTCATTCAAGT

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 8
-cgaaactttttcacatacatgatgctattttctggaagtaattt---attttgtgtttcttactatctgaacaaagttaataattcttcttgtttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
  |||| |||   | |||  |  | ||   || |  |  | ||||   |  || |    |||  ||||  ||  ||||||||   | ||    ||| ||| |||||||||||||||||||||||||||||| |||||||||||||
atgaaaatttacta-ataggttttacttgcttgtttagattatttaagaacttttccaccttgttatccaaaagaagttaat---ttttggattttatttgcagCTATTTACCTGAGGAGATGAGGAACCCTACTACCTTCAAAT

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 11
---cgaaactttttcacatacatgatgctattttctggaa-gtaatttattttgtgtttcttactatctgaacaaagttaataattcttcttgtttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
     ||| ||  | | |    | |    ||| | | ||   ||    |  || |  | |||  ||||  ||  |||||||      ||   ||||  || |||||||||||| ||||||||||||||||| |||||||||||||
gatgaaaatttactgataggttttacttgattgtttagattatataagaacttttcctccttgttatccaaaagaagttaaa----ttttgggttttattgcagCTATTTACCCGAGGAGATGAGGAACCCTACTACCTTCAAAT

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|30137643|gb|CB922981.1|CB922981
EST:     GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
EST: gi|110369051|gb|EC933194.1|EC933194
EST:     GCTCTGGAGAAAATGATGG-AGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
EST: gi|37183876|gb|CF603230.1|CF603230
EST:     GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
EST: gi|30136598|gb|CB921936.1|CB921936
EST:     GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
EST: gi|32268986|gb|CD718145.1|CD718145
EST:     GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
EST: gi|30136267|gb|CB921605.1|CB921605
EST:     GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
EST: gi|30126394|gb|CB911733.1|CB911733
EST:     GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC                         CTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
genomic: GCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCCgtaatatagt ... ttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgtttcttactatctgaacaaagttaataattcttcttgtttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT
                                   ttcttcttgtttcttt  CT-rich tract
                     aacaaagttaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgaaactttttcacatacatgatgctattttctggaagtaatttattttgtgtttcttactatctgaacaaagttaataattcttcttgtttctttacagCTATTTACCTGAGGAGATGAGGAACCCCACTACCTTCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - -cacatac
- - - - - - - - - -tgatgct
- - - - - - - - - - - - - - tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaa