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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttttggcttagtccttcttgtcatattgttatataggatttttttattttttgtttttcaattaaatactttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02760.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 4
--------------------gtgttttggcttagtccttcttg--tcatattg-ttatataggatttttttattt--tttgtttttcaattaaatactttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG
                     ||| ||    ||||  |||     | || ||| || || || ||  ||    |   | | |||    |  |  || |||  | |     ||   | ||   |||||||||||||||||||||||||| ||||||||||||||||| || || |||||||| |||
gttacttctccattgccttattgtcttttagtagtagttccaaattgatgttgattttacagtatggttaggctaggtctatttcctgaaaacttagtttgttaattaactgcattattcatcagGTTTTTGAAGGAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 4
-----------------------gtgttttggct-tagtccttcttgtcatattgttatataggatttttttattttttgtttttcaattaaa--tactttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG
                       || |||| ||  |||| ||  ||    | |  || |  || ||  |  | ||  ||   || | |  |||  || |||  | |     ||   | ||   ||||| |||||||||||||||||||| ||||||||||||||||| || || |||||||| |||
gttacttctccattctcctgattgttttttagcagtagttctaatttgattttgattctgcagtatggtcatgttagttccattcccagaaaacttagtttgttaattaactgcattattcatcagGTCTTTGAAGGAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------gtgttttg--gcttagtccttcttgtcatattgttatataggatttt-tttattttttgtttttcaattaaatact--ttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG
                                                   ||||  ||||| |    |   |  | |   |  ||   || ||   || |  || || |||||   | | |    ||     |||   ||   ||| |||||| ||||| ||||| |||||||| |||||||| ||||||||||| ||||||||||| |||
gtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatt-tgtaaatcaatgtaatcttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccagGTATTTGAGGGAACATCTGGAATCGACAACAAGTACACAACTGTGCAATTTACAGGAGAG

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|30327898|gb|CD011160.1|CD011160
EST:     AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|110730165|gb|EE106929.1|EE106929
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|71862417|gb|DT011472.1|DT011472
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|71861168|gb|DT010223.1|DT010223
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|30325484|gb|CD008746.1|CD008746
EST:     AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|32267904|gb|CD717063.1|CD717063
EST:     AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|56409259|gb|CX017511.1|CX017511
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|71864966|gb|DT014021.1|DT014021
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|30323990|gb|CD007252.1|CD007252
EST:     TCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: TCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|32248996|gb|CD714815.1|CD714815
EST:     AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|71859980|gb|DT009035.1|DT009035
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|110357277|gb|EC920703.1|EC920703
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|32249022|gb|CD714841.1|CD714841
EST:     AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: AAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|46917753|gb|CN547082.1|CN547082
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|71861589|gb|DT010644.1|DT010644
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|56409525|gb|CX017777.1|CX017777
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
EST: gi|56409500|gb|CX017752.1|CX017752
EST:     CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG                         GTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT
genomic: CTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgtgattactg ... ttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttttgtttttcaattaaatactttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG
                                          ttgtttt  CT-rich tract
     tttttgtttttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttttggcttagtccttcttgtcatattgttatataggatttttttattttttgtttttcaattaaatactttactcagcttatgttgttttggccagGTTTTTGAAGGAACTTCTGGAATTGACAACAAATACACAACTGTTCAATTTACAGGGGAG

- - - tggctta
- - - - - - - tccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg