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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgataagcttttctcagtgtgtttccattacttaataatgttagaccctcgggttttacttgctttgctttaatgtcttataatctgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTGATCCTTATCCTGAGGAACAGGTTGAAGTATGCTCTCACATATCGTGAGG

Basic information

species Vitis vinifera
transcript Vv06s0004g07150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G06440.1 (Glycine max), 3'ss of exon 2
gtaagtgataagcttttctcagtgtgtttccattacttaataatgttagaccctcgggttttacttgc----tttgctttaatgtcttataatctgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTGATCCTTATCCTGAGGAACAGGTTGAAGTATGCTCTCACATATCGTGAGG
               |    |  ||  |  || |  || || || |||          ||||| |||     || | || ||    || |     |   |  |||| || |||||||| |||||||| || ||||| ||||||||  | || |||||||| |||||  |||||||| | ||||||||||| |||||| | || |
--------------gtatgtacagtactcacagttgttgatgatatta--tttgtcatttttatttgtaattttcgtttgaactcattttgcctggctgtgtagGCACCGAAGCCATCATCTGGACCCCACAAGTCCAGGGAGTGTCTTCCTTTGATCCTCATCCTACGGAACAGGCTAAAGTATGCTCTAACATATAGAGAAG

upper sequence: Vv06s0004g07150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S38_194V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagtgataa-gcttttctcagtgtg--tttccattacttaataatgttagaccctcgggttttacttgctttgctttaatgtcttataatctgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTGATCCTTATCCTGAGGAACAGGTTGAAGTATGCTCTCACATATCGTGAGG
  || || |    || ||   ||||    | | ||| |  |     |  | |  ||| |    |  |  || ||  ||| |||   | |  |||||    ||||| |||||||||||| ||||||| || |||  |||||| |||||||||||| |  | || ||||| || ||  |||||||||| || || || |||||||
--aattgtttccactgttgatagtgaagatcttcatgagctctacgttcttgtacctggttgatgccacgcattattttgatgatatttg-tctgtttctcagGCCCCCAAGCCATCTCCTGGACCACACAAGGAAAGGGAATGCTTGCCCTTGGTTGTGATGCTGAGAAATAGACTGAAGTATGCCCTGACCTACCGTGAGG
















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|110702679|gb|EE078871.1|EE078871
EST:     GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTT                         GCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
genomic: GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgata ... tgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
EST: gi|30296893|gb|CB973687.1|CB973687
EST:     GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTT                         GCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
genomic: GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgata ... tgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
EST: gi|110701173|gb|EE078481.1|EE078481
EST:     GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTT                         GCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
genomic: GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgata ... tgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
EST: gi|33406463|gb|CF212090.1|CF212090
EST:     GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTT                         GCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
genomic: GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgata ... tgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
EST: gi|110688373|gb|EE066853.1|EE066853
EST:     GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTT                         GCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
genomic: GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgata ... tgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
EST: gi|110700067|gb|EE077679.1|EE077679
EST:     GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTT                         GCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG
genomic: GGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTTGGGGGTGCATTTgtaagtgata ... tgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaccctcgggttttacttgctttgctttaatgtcttataatctgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTGATCCTTATCCTGAGGAACAGGTTGAAGTATGCTCTCACATATCGTGAGG
                           ctttaat  putative branch site (score: 4)
                            tttaatgtcttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgataagcttttctcagtgtgtttccattacttaataatgttagaccctcgggttttacttgctttgctttaatgtcttataatctgtcatacagGCTCCCAAGCCATCTTCTGGACCTCATAAGTCAAGGGAGTGCTTGCCCTTGATCCTTATCCTGAGGAACAGGTTGAAGTATGCTCTCACATATCGTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG