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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatgggggaggaacaaaattctcttggacaatctctaaagaggagatgttacatctctttgattttggttgcacatactcttgaacaaattcatggaactatgtgaatataatttaccaagaaaatttgttacacag

Basic information

species Vitis vinifera
transcript Vv14s0036g01460.t01
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g01460.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: GLYMA20G37100.1 (Glycine max), 5'ss of exon 29
GTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatgggggaggaacaaaattctcttggacaatctctaaagaggagatgttacatctctttgattttggttgcacatactcttgaacaaattcatggaactatgtgaatataatttaccaagaaaatttgttacacag
|||||| || |  ||||| ||||||||||| |||||| ||||||||||||||||||| || || || |||||||| ||||||||     | ||      |||| |||  || |  | ||        | || |     | ||    || || |||                                                               
GTATGGGCAGAAAAAGCCTGTGTTTGCTTATCGATTGCTGGCTCATGGAACTATGGAGGAGAAGATATATAAGCGCCAGgtaatacaacatga-tgtgcttctattgttcatttgccaat-------tttttctaacttgtggaaatgatttcactag------------------------------------------------------------

upper sequence: Vv14s0036g01460.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: AT1G08600.1 (Arabidopsis thaliana), 5'ss of exon 26
GTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatgggggaggaacaaaattctcttggacaatctctaaagaggagatgttacatctctttgattttggttgcacatactcttgaacaaattcatggaactatgtgaatataatttaccaagaaaatttgttacacag
|||||||||||  ||||| || ||||| ||| |||||||||| | ||| ||||| ||||||||||| ||||| ||||||||| ||    ||| | ||||   | |||   ||| |          | |||| | |  |||  |          | | | || ||||  |  ||         ||| ||||| |||                       
GTATGGCCAAAAGAAGCCCGTATTTGCGTACAGATTGATGGCACGTGGGACTATTGAAGAAAAAATATATAAACGTCAGgtattgaa--aggcataaaacaatgttg---aatttt---------gctgtttctttccttcaa--------agagacattcatgaatcagatc---------tgttaatatgattag---------------------
















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|161710320|gb|FC059834.1|FC059834
EST:     ACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG                         GTGACAAAGGAAGGCCTTGCTGCCAGGGTGGTCGA
genomic: ACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatggggg ... tgttacacagGTGACAAAGGAAGGCCTTGCTGCCAGGGTGGTCGA
EST: gi|29785711|gb|CB342999.2|CB342999
EST:     ACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCTG                         GTGACAAAGGAAGGCCTTGCTGCCAGGGTGGTCGATAGACAACAAGTACAT
genomic: ACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatggggg ... tgttacacagGTGACAAAGGAAGGCCTTGCTGCCAGGGTGGTCGATAGACAACAAGTACAT
EST: gi|161713628|gb|FC062542.1|FC062542
EST:     ACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG                         GTGACAAAGGAAGGCCTTGCTGCCTGGGTGGTCGATAGACAACAAGTACAT
genomic: ACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatggggg ... tgttacacagGTGACAAAGGAAGGCCTTGCTGCCAGGGTGGTCGATAGACAACAAGTACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAGgtaatgggggaggaacaaaattctcttggacaatctctaaagaggagatgttacatctctttgattttggttgcacatactcttgaacaaattcatggaactatgtgaatataatttaccaagaaaatttgttacacag

- - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA