Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcttcctttttccccccttgtttttttcctgtagttgggtgttgtggttgggtgtagtgaactgattgacatctttctatgtttcattttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTCTTGGGATTTGGACCTTTGATCCTCATAACTGTTGCATTCTTCTGTGCTC

Basic information

species Vitis vinifera
transcript Vv03s0088g00400.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0088g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G27290.1 (Glycine max), 3'ss of exon 2
-cttgcttccttttt---ccccccttgtttttttcctgtagttgggtgttgtggttgggtgtagtgaactgattgacatctttctatgtttcattttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTCTTGGGATTTGGACCTTTGATCCTCATAACTGTTGCATTCTTCTGTGCTC
   ||  |  ||||        | ||| |  |||  | || |||  | | ||  |||||    ||||| |       |      || || |   | ||||||||||| |||| || || ||||||||| |  | |||||||||||||||||||||||||||||||| || ||||||||||||| |||||||  ||| | |||||
taatgtattattttggagtgagctttgatgctttgatctaattgaatttcgtttttggg----gtgaaatcccaagaaatcacatacgtatttatctatttcagGGCTTGATACCTCGTGCTAAACTTCTTTTGACAATTGGAGGAACATTCTTCTTGGGATTTGGGCCGTTGATCCTCATAATTGTTGCAACCTTTTCTGCTC

upper sequence: Vv03s0088g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G40120.1 (Glycine max), 3'ss of exon 2
----cttgcttcctttttccccccttgtttttttcctgtagttgggtgttgtggttgggtgtagtgaactgattgacatctttctatgtttcattttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTCTTGGGATTTGGACCTTTGATCCTCATAACTGTTGCATTCTTCTGTGCTC
    ||    |  | | |          |    |    |  ||   || | |  |||  | | ||     |  ||| |||  | || || |   |  |||||||||| || | || || ||||||||| |  | |||||||||||||||||||||||||||||||| || ||||||||||||| |||||||   || | |||||
agaactaatataatgtattattttgaagtgagctttgatgctt---tgatctaattgaattttgtttttggggtgaaatcact-tacgtatttatccatttcagGGCTTGGTACCTCGTGCTAAACTTCTTTTGACAATTGGAGGAACATTCTTCTTGGGATTTGGGCCATTGATCCTCATAATTGTTGCAACTTTTTCTGCTC
















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|30134271|gb|CB919609.1|CB919609
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|37184574|gb|CF603928.1|CF603928
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|32269456|gb|CD718615.1|CD718615
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|30130543|gb|CB915882.1|CB915882
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|110383842|gb|EC948243.1|EC948243
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|111125038|gb|EE253663.1|EE253663
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|110687557|gb|EE065101.1|EE065101
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|110377814|gb|EC942903.1|EC942903
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
EST: gi|30125183|gb|CB910522.1|CB910522
EST:     TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAG                         GGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC
genomic: TATCTAATCAAAGGGAGCGCTCCATGGCGTTGAACAGTGAAGGCCTTGAGgtttagacat ... tttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggttgggtgtagtgaactgattgacatctttctatgtttcattttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTCTTGGGATTTGGACCTTTGATCCTCATAACTGTTGCATTCTTCTGTGCTC
                     gattgac  putative branch site (score: 3)
                                       tttcattttatttc  putative PPT
                               tttctatgtttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcttcctttttccccccttgtttttttcctgtagttgggtgttgtggttgggtgtagtgaactgattgacatctttctatgtttcattttatttcagGGCCTGATTCCACGGGCTAAACTTTTGCTAACAATTGGAGGAACATTCTTCTTGGGATTTGGACCTTTGATCCTCATAACTGTTGCATTCTTCTGTGCTC

- tgcttcc
- - - - - - - cccccct
- - - - - - - - - - - - - - ttcctgt
- - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg