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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgagttaggggaattaaacctatggctattacatattagtttcttttttccatgagaaggttttgattaatacaccttgttctgttcgttattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATGGCTCAAAGTAGAATACTGCTGTTTTGGTATTTCACCACTTACCGTCTCC

Basic information

species Vitis vinifera
transcript Vv01s0011g04670.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 10
acgagttaggggaattaaacctatggctattacatattagtttcttttttccatgagaaggttttgattaatacaccttg---ttctgttcgttattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATGGCTCAAAGTAGAATACTGCTGTTTTGGTATTTCACCACTTACCGTCTCC
   | |||    || ||    | ||  | |    | | ||  | | | | |  |    |    |     |   ||| |||   |||  |||  | |||| |||||||| |||||  | || ||||||   ||| | ||||| ||||| ||||| || |||| |||||||||||| |||||||||| |||||| |||| |||||
--caattatacaaaatacctatctgcttttccactgtcagaatatatgtgctttcttgaatgctgatccagctcactttggtattcccttccct-ttttacagGCACTAGAGCGTATTTCCTTTGGAAAAAGTAGGATTAGGGATACGGTGATAGCACAAAATAGAATACTGCTATTTTGGTATTGCACCACCTACCTTCTCC
















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|110387100|gb|EC951743.1|EC951743
EST:     GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAG                         GCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG
genomic: GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAGgtaaagggag ... tattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG
EST: gi|34549698|gb|CF517930.1|CF517930
EST:     GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAG                         GCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTANAGATACAGTGATG
genomic: GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAGgtaaagggag ... tattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG
EST: gi|34544781|gb|CF513013.1|CF513013
EST:     GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAG                         GCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG
genomic: GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAGgtaaagggag ... tattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG
EST: gi|110372843|gb|EC937037.1|EC937037
EST:     GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAG                         GCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG
genomic: GTCTTGAATTTGATCACCAGCAGCCATTTGATATTCAAACTGGAGAACAGgtaaagggag ... tattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccatgagaaggttttgattaatacaccttgttctgttcgttattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATGGCTCAAAGTAGAATACTGCTGTTTTGGTATTTCACCACTTACCGTCTCC
                    gattaat  putative branch site (score: 3)
                                            ttatttt  putative PPT
                ttttgattaataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgagttaggggaattaaacctatggctattacatattagtttcttttttccatgagaaggttttgattaatacaccttgttctgttcgttattttgcagGCACTTGAGCGGCTCTCATTTGGAGGCAGTCGCATTAGAGATACAGTGATGGCTCAAAGTAGAATACTGCTGTTTTGGTATTTCACCACTTACCGTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -aggggaat
- - - - - - - - aaaccta
- - - - - - - - - - - -tggctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatacac