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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatcatttcgtcgcaaattttggttatgcttacataaatccagggtacattgacattgtcttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g08150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g08150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g13810.1 (Oryza sativa), 3'ss of exon 2
--------------------------gtatacatcatttcgtcgcaaattttggttatgcttacataa--atccagggtacattgacattgtcttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG
                           ||   | ||  | | |    ||     | ||| ||   |    ||| |       ||   |||     || |||||| ||  ||||||||||||| || || |||||||||| ||| ||||| ||   |||| ||||||||||||  || ||||| |  ||||||||| ||||||
cttccctttatatttttgttctgattttaactaccaccttggcttggatgc-actcatgtttgtttggttatctaatagctgttataattaatcctt-acagGAGACGGCATTTATAGAGCAGCTTGTAGAAGATGAAACTCATATGGAGGGCGTACCTCCTGGTTGTTCAAAAATTATGAATTTTCATCTTCATCTGGAAG

upper sequence: Vv18s0001g08150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G179504_T02 (Zea mays), 3'ss of exon 2
---gtatacatcatttcgtcgc-aaattttggttatgctta-------cataaat-----ccagggtac-----attgacattgtc-----ttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG
    ||||  | |||  |   | ||||| |  |||| | ||       ||||| |     |   | | |     ||||| |||  |     |    ||||| ||| |||||||||||||| || || |||||||||| ||| ||||| || | |||  ||||||||||||  || |||||     ||||||   | ||||
cccatatattttattctgaaactaaattctatttatacctatcgttcacataagtaataactgtgctccttctgattgaaattagcaatgatacatacagGCAACAACATTTATAGAGCAGCTTGTAGAAGATGAAACTCATATGGAGGGCATACCAACTGGTTGTTCAAAAATTATGAATGTTAATCTTCGCCTAGAAG

upper sequence: Vv18s0001g08150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G179504_T01 (Zea mays), 3'ss of exon 2
------------------gtatacatcatttcgtcgc-aaattttggttatgctt-------acataaat-----ccagggtac-----attgacattgtc-----ttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG
                   ||||  | |||  |   | ||||| |  |||| | |       |||||| |     |   | | |     ||||| |||  |     |    ||||| ||| |||||||||||||| || || |||||||||| ||| ||||| || | |||  ||||||||||||  || ||||| ||  |              
tcttcctaagtcatccccatatattttattctgaaactaaattctatttatacctatcgttcacataagtaataactgtgctccttctgattgaaattagCAATGATACATACAGGCAACAACATTTATAGAGCAGCTTGTAGAAGATGAAACTCATATGGAGGGCATACCAACTGGTTGTTCAAAAATTATGAA-TGTTA--------------

upper sequence: Vv18s0001g08150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G09470.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------gtatacatcatttcgtcgcaaattttggttatgcttacataaatccagggtacattgacattgtcttt----tcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG
                                                                          |  | ||  ||        ||| |    |    ||     |||| |   || | ||| ||    |||    | |||||| ||||| |||||||| ||| ||||||||||||||||||||||||||||  ||||| ||||||||||||  ||| |||| |||||||| |||||||  |
gtatgcctcctattgtctctctttaatctgtccctacctattaatatgttcagatgtcctattgtccttactatttcatatttttagccatttaatatcatctgcaattgttataatcaa---taaactgatatgacttttggtttgacagGAGACCACCTTTATAGAACAATTGGTGGAAGATGAAAGTCAAATGGAAGGTTCACCTCCTGGTTGTTCAAAAATATTGAATTGGCATCTCCATTTGGCTG

upper sequence: Vv18s0001g08150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G09560.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------gtatacatcatttcgtcgcaaattttg-gttatgcttacataaatccagggtacattgacattgtcttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG
                                                                     |||  |     | |   | ||  |  |  || |||| |   ||  |    | || ||| ||    ||| |||||| ||||| |||||||| ||| ||||||||||||||||||||||||||||  ||||| ||||||||||||  ||| |||| |||||||| ||||||   |
gtatgcctcctattgtcactctttaatctgtccctacctattaatatgttcagatgtccttgctatttcatatttttagccatttaatatcatatgcaattcttataatcattaaactgatat-gacttttgggtttgacagGAGACCACCTTTATAGAACAATTGGTGGAAGATGAAAGTCAAATGGAAGGTTCACCTCCTGGTTGTTCAAAAATATTGAATTGGCATCTCCATTTGACTG

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|71884768|gb|DT033823.1|DT033823
EST:     CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAA                         GAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
genomic: CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAAgtatacatca ... cttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
EST: gi|71889916|gb|DT038971.1|DT038971
EST:     CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAA                         GAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
genomic: CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAAgtatacatca ... cttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
EST: gi|71889101|gb|DT038156.1|DT038156
EST:     CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAA                         GAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
genomic: CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAAgtatacatca ... cttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
EST: gi|351025492|gb|FQ435184.1|FQ435184
EST:     CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGGAGGAGGGTTTCCAA                         GAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
genomic: CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAAgtatacatca ... cttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
EST: gi|351038791|gb|FQ464657.1|FQ464657
EST:     CCACTTCAGCTCCCATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAA                         GAAACCACATTTATAGAGCAACTGGTGGAAGATGAAA-TCAAATGGAAGGG
genomic: CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAAgtatacatca ... cttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG
EST: gi|110699782|gb|EE077082.1|EE077082
EST:     CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAA                         GAAACCACATTTATAGAGCAACTAGTGGAAGATGAAAGTCAAATGGAAGGG
genomic: CCACTTCAGCTCCAATTCAACAGTTGGACACAGTGAAGGAGGGTTTCCAAgtatacatca ... cttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattttggttatgcttacataaatccagggtacattgacattgtcttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG
                                         ttgtcttttc  CT-rich tract
               ttacataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacatcatttcgtcgcaaattttggttatgcttacataaatccagggtacattgacattgtcttttcacagGAAACCACATTTATAGAGCAACTGGTGGAAGATGAAAGTCAAATGGAAGGGACACCTGCTGGTTGTTCAAGGATAATGAACTGGCATCTTCATTTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG