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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaaatgaattcttgtcatcttccatcgcgattctgatatgtcatttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA

Basic information

species Vitis vinifera
transcript Vv02s0025g02260.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02260.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g47970.1 (Oryza sativa), 3'ss of exon 1
----aagaaatgaattcttgtcatcttccatcg----cgattctgatatgtcatttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA
    |   | |||   |     |   | ||| |    | ||| |   |      |||| ||     ||   |  |||   ||| |  ||  ||||  |     ||||| | || || || |  |||||||||||||||||||| || || || ||||||||||| || || |||||  | || |||||||||||||| |||| |||||
cttgacatagtgagaacagagaaaactgcattggattcaattgtagaagaaagattttcctccctatt---gccactgcctactaactgaattttaat-----tgcagATGACATACCATTTTTTTCACTGGAAGAAGGGAACTCCGTTTGCTGATGACCAGGGGATGTATAATAGATTGACTTGGTGGGAGCAAATGGACAATGGGA

upper sequence: Vv02s0025g02260.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
aagaaatgaattcttgtcatcttccatc-gcgattct-gatatgtcatttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGG---ATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA
| |   ||| ||   |   ||| | ||  |   | ||  | ||     |  |  |  ||  |  |||   | | || | |||   ||  | |  |   |||| | |||||||||| ||| || |||||||||||||| ||||| || |   ||||||| || |||||||| || ||||| |||||||| ||||| || |  |   
agggcttgagtta--gatgtctacaatttgtagtcctcaacattcagctactagtactacatactgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG---

upper sequence: Vv02s0025g02260.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g45180.1 (Oryza sativa), 3'ss of exon 1
aagaaatgaattcttgtcatcttccatcgcgattctgatatgtcat----ttttgcttgtagt-tcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA
    | |    ||||  ||| |||  | ||  ||||  |||  |||    |  | | |   || ||   | | ||   ||    | |  |  | |  |  | ||| | || || ||||  || || ||||||||||||||||| || || ||||||||||| || ||||| |   | || |||||||||||||| |||| ||| |
----actattctctttgcattttcgttagcatttctc-tatagcatcggatgatacctaccgtgtccaatgatttcccacttaatcgaataatcttatgtttcagATCACATACCACTTTTTCCATTGGAAGAAGGGAACACCTTTTGCTGATGACCAGGGAATGTACAACACATTGACTTGGTGGGAGCAAATGGACAATGGCA

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|77579802|gb|DV218780.1|DV218780
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
EST: gi|71868218|gb|DT017273.1|DT017273
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
EST: gi|71866545|gb|DT015600.1|DT015600
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
EST: gi|110381919|gb|EC938009.1|EC938009
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
EST: gi|71873092|gb|DT022147.1|DT022147
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
EST: gi|110410892|gb|EC976586.1|EC976586
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
EST: gi|71876002|gb|DT025057.1|DT025057
EST:     GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTG                         GTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC
genomic: GCTGCTCCTCCGGCGCCGCCTGGACCATTCTCCACCTCTCCCATTTCCTGgtatacgctt ... cgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA
                     acttaat  putative branch site (score: 4)
                                      tttttgtc  putative PPT
                   ttacttaatacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaaatgaattcttgtcatcttccatcgcgattctgatatgtcatttttgcttgtagttcatgttacttaatacaatttgggtttttgtcgtcctgcagGTTACTTATCACTGCTTTCACTGGAAGAAGGGAACACCATTCGCGGATGACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- -aaatgaa
- - - - - - - - - - cttccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatacaa