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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgttaattttatcagtgagtgcaccctgttttacaattctaaatgttaaggtttcaaactatgctgcaaagttctcattcttagtcattttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGATATATATGACACAGATGGAAGCAGTGTAGTAGCAGCTTCAGAACCTCTG

Basic information

species Vitis vinifera
transcript Vv05s0077g00060.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00060.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G34110.1 (Glycine max), 3'ss of exon 10
tatgttaattttatcagtgagtgcaccctgttttacaattctaaatgttaaggtttcaaactatgctgcaa--agttctcattcttagt---cattttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGATATATATGACACAGATGGAAGCAGTGTAGTAGCAGCTTCAGAACCTCTG
||  | ||   |   |  | || |   |||| ||| |||| |   | |     ||   |||||| ||  |   || |   | |  || |    ||| ||| |||||||||| ||||| || |||||||||||||||||| |||||||| |||| ||||||  ||| ||||||||||| |||| | ||||| |||||||||| |||
ta-atcaacaatggaaaag-gttctttctgtattaaaattttctttttcttaatt---aactatcctatattcagcttgaagttctaatatatattatcaaccagGTTGGACAAAGGGGTGATTGTGTATATTTGTGATAGTCGTGGTGTTCGAGATATACTTGATACAGATGGAAGTAGTGCACTAGCAACTTCAGAACCCCTG

upper sequence: Vv05s0077g00060.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G17740.2 (Arabidopsis thaliana), 3'ss of exon 9
tatgttaattttatcagtgagtgcaccctgttttacaattctaaatgttaaggtttcaaactatgctg-caaagttctcattcttagtcattttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGATATATATGACACAGATGGAAGCAGTGTAGTAGCAGCTTCAGAACCTCTG
  |  |||  | || |     | ||   | |     | |   |||| | ||| |    | ||||  |   | |    |||   || |  ||   ||    |||| || ||||| || |||||||||||||| ||| |||| ||| || | ||||||||||| || |||||||||| ||   ||||| | || || ||||| 
-gtaataacctcataaaccgttaca---tataacgaattagaaaatttcaagatccacagctatcataatagaaacttcaacatttgctatccaca----gGTTAGATAAAGGAGTGATTGTGTATATTTGCGATAGTCGAGGTGTTAGAGATATATATGATACTGATGGAAGCAATGCTATAGCAACCTCTGAGCCTCTT
















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|349821096|gb|FQ404349.1|FQ404349
EST:     TGGTGGCCTTTTCCCAGAGGGAGTTGAGATTGCTAAGATTTG                         GTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGA
genomic: TGGTGGCCTTTTCCCAGAGGGAGTTGAGATTGCTAAGATTTGgtaagctcca ... tttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGA
EST: gi|349809249|gb|FQ399023.1|FQ399023
EST:     TGGTGGCCTTTTCCCAGAGGGAGTTGAGATTGCTAAGATTTG                         GTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGA
genomic: TGGTGGCCTTTTCCCAGAGGGAGTTGAGATTGCTAAGATTTGgtaagctcca ... tttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGA
EST: gi|351036039|gb|FQ463884.1|FQ463884
EST:     TGGTGGCCTTTTCCCAGAGGGAGTTGAGATTGCTAAGATTTG                         GTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGA
genomic: TGGTGGCCTTTTCCCAGAGGGAGTTGAGATTGCTAAGATTTGgtaagctcca ... tttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaggtttcaaactatgctgcaaagttctcattcttagtcattttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGATATATATGACACAGATGGAAGCAGTGTAGTAGCAGCTTCAGAACCTCTG
                                            ttttcatcc  CT-rich tract
                                           attttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgttaattttatcagtgagtgcaccctgttttacaattctaaatgttaaggtttcaaactatgctgcaaagttctcattcttagtcattttcatccagGTTGGAAAAAGGTGTAATTGTGTATATTTGTGATGGTCGTGGTATTCGTGATATATATGACACAGATGGAAGCAGTGTAGTAGCAGCTTCAGAACCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - -tgcaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgct