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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGTACAATCGGTGGACTTCTCCTTATCTTGACCGTGATGCTGAGGCAGTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcag

Basic information

species Vitis vinifera
transcript Vv03s0091g00080.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G464137_T03 (Zea mays), 5'ss of exon 3
CTCAGTACAATCGGTGGACTTCTCCTTATCTTGACCGTGATGCTGAGGCAGTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcag
|  | |  ||||||||||| || |||||||| |||   ||||||||||||||||| |||||| |     | ||| | ||||| || | | ||||||| ||||| |             ||||||| |         |||  ||| || |      |   |   |||  ||||| |      |  |   | |  |||   |  | |  |  |             
CCAAATTTAATCGGTGGACCTCGCCTTATCTCGACAAAGATGCTGAGGCAGTTCGCGAGGATGATGAGCTCAAGTTGGAAGTAGCTGGGCTGAAATCGATgtaat-------------tacctcactg--------aattgaaattagtg--gccacctgtgttttgtttctgtacatgggaattgtgactttttttggtttccaactgcag------------

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G40730.1 (Glycine max), 5'ss of exon 3
CTCAGTACAATCGGTGGACTTCTCCTTATCTTGACCGTGATGCTGAGGCAGTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcag
|||| || ||||| |||||||| || ||||| || |||||||||||||||||||| || || ||     |||||||||||||||| ||| ||||||||| ||| |        || | |  ||  ||| |   | | ||||  | || || | ||  |||   |||  ||   | | |   | |||    |                                 
CTCAATATAATCGTTGGACTTCCCCCTATCTCGATCGTGATGCTGAGGCAGTTCGGGAAGACAATCCGCTGAAGCTTGAAGTTGCTGAGCTGAAATCTAAgtatt--------attactcacttttttttacccattatatgcagtagttttgttgttagattttttctttataggaatttatgttcctgtag-------------------------------

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G26580.1 (Glycine max), 5'ss of exon 3
CTCAGTACAATCGGTGGACTTCTCCTTATCTTGACCGTGATGCTGAGGCAGTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcag
|||| || ||||| || ||||| || |||||||| |||||||||||||| ||||| || || ||  |  |||||||||||||||| ||| ||||||| | ||| ||   |  |       | |  ||| |   | | ||||    || ||   ||  ||| | |||   | |  || ||     ||    |||| |                            
CTCAATATAATCGTTGTACTTCCCCCTATCTTGATCGTGATGCTGAGGCTGTTCGGGAAGACAATCTGCTGAAGCTTGAAGTTGCTGAGCTGAAATCCAAgtattgtggctct-------ctttgtttttacccattatatgctgtagtttcgttgttag-attttttctttataggaat----ttatggtcctgtag--------------------------

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|161714716|gb|FC064488.1|FC064488
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATAC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATAC
EST: gi|30324984|gb|CD008246.1|CD008246
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|32248279|gb|CD714098.1|CD714098
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|110727535|gb|EE104406.1|EE104406
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|33403054|gb|CF208681.1|CF208681
EST:     AGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: AGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|32269752|gb|CD718911.1|CD718911
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|33402966|gb|CF208593.1|CF208593
EST:     GTTCGAGAGGATAACATTCTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|30326383|gb|CD009645.1|CD009645
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
EST: gi|32247178|gb|CD712997.1|CD712997
EST:     GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTAT                         GTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC
genomic: GTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttc ... tattttgcagGTTCTGTGAGAGATCACAAGCCCTAGTACATGGAGATCTTCATACTGGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAGTACAATCGGTGGACTTCTCCTTATCTTGACCGTGATGCTGAGGCAGTTCGAGAGGATAACATTTTGAAGCTTGAAGTTGCCGAGTTGAAATCTATgtagtgcttccatatcagtacctcatttctttacgtaatataaaatatttctattaatagcagtttaattctgaagtaaacaggttgaaatcctttctatgcctagttagaatctattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG