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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatgaacacttttaaggtgatattttgttgaatacattggttaatttcctcaagcctttttcagtggacatggttgtgtgtgttgttatggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCTGTTCTTGTGCATGGCATTCTAGGTAGCCGGAAGAACTGGG

Basic information

species Vitis vinifera
transcript Vv18s0001g06010.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G007160_T02 (Zea mays), 3'ss of exon 3
--aatatgaacactttta-aggtgatattttgttgaatacattggttaatttcctcaagccttttt---cagtggacatgg-ttgtgtgtgttgttatggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCTGTTCTTGTGCATGGCATTCTAGGTAGCCGGAAGAACTGGG
  ||  |   || |     |  | || | |  ||   |  |    |   ||   |      |||||   || | |||||   |    |       | |    | |||||    |||| |||  ||   ||||| ||||| |||||||| ||||||||||||||| | |||||||| || || ||| |||| |||||||
gtaagttttgcattcacgcaaattatctgtcattagttgtaaaactagcttgattttgatttttttgtccaatcgacataaatcaaattcaacactttaactt-cagGTTCAGTGGAATTCATTTATGGACAAATCAATACCTGATCCACCAACAGCTGTTCTTCTTCATGGCATCCTTGGGAGCAGGAAAAACTGGG

upper sequence: Vv18s0001g06010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G007160_T03 (Zea mays), 3'ss of exon 3
--aatatgaacactttta-aggtgatattttgttgaatacattggttaatttcctcaagccttttt---cagtggacatgg-ttgtgtgtgttgttatggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCTGTTCTTGTGCATGGCATTCTAGGTAGCCGGAAGAACTGGG---------
  ||  |   || |     |  | || | |  ||   |  |    |   ||   |      |||||   || | |||||   |    |       | |    | |||||    |||| |||  ||   ||||| ||||| |||||||| ||||||||||||||| | |||||||| || || ||| |||| |||||||         
gtaagttttgcattcacgcaaattatctgtcattagttgtaaaactagcttgattttgatttttttgtccaatcgacataaatcaaattcaacactttaactt-cagGTTCAGTGGAATTCATTTATGGACAAATCAATACCTGATCCACCAACAGCTGTTCTTCTTCATGGCATCCTTGGGAGCAGGAAAAACTGGGGTAAATGAG
















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|352776833|gb|FQ472720.1|FQ472720
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352773576|gb|FQ472358.1|FQ472358
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352769737|gb|FQ468665.1|FQ468665
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352768560|gb|FQ467516.1|FQ467516
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352781488|gb|FQ468332.1|FQ468332
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352781638|gb|FQ468936.1|FQ468936
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352781598|gb|FQ468896.1|FQ468896
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|352776761|gb|FQ472648.1|FQ472648
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
EST: gi|71873371|gb|DT022426.1|DT022426
EST:     GCATATGATCTTGTTCAAGGACCACTT                         GTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT
genomic: GCATATGATCTTGTTCAAGGACCACTTgtaagtcgtg ... tggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcctcaagcctttttcagtggacatggttgtgtgtgttgttatggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCTGTTCTTGTGCATGGCATTCTAGGTAGCCGGAAGAACTGGG
 ggttaat  putative branch site (score: 4)
             tttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatgaacacttttaaggtgatattttgttgaatacattggttaatttcctcaagcctttttcagtggacatggttgtgtgtgttgttatggtgtgcagGTAAGATGGAGTTCTATTGCAGACAAGTCAATTCCTGATCCTCCAACAGCTGTTCTTGTGCATGGCATTCTAGGTAGCCGGAAGAACTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- tatgaac
- - - - - - - - - - - - - - - -gaataca
- - - - - - - - - - - - - - - - - - - - - - - - tcctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg