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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCATTTGTTGCAATCGGGGCAACGATGGTTGGTAGCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaattcatttttttatctcttttatttttcattgtggtgtccatgtattctgctatgcttctaattaacattctaccttcatttgctcatttacag

Basic information

species Vitis vinifera
transcript Vv12s0055g00710.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00710.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA08G19310.2 (Glycine max), 5'ss of exon 18
GTGGCATTTGTTGCAATCGGGGCAACGATGGTTGGTAGCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaattcatttttttatctcttttatttttcattgtggtgtccatgtattctgctatgcttctaattaacattctaccttcatttgctcatttacag
||||||||||||||||| || || || |||||||||||||| || || || || || ||||||||||||||  |||| ||||| ||||||    |        || ||  |  || |||   ||  |       || | || | || || |||||| | || ||     ||  |||    ||||||||
GTGGCATTTGTTGCAATTGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAGgtttggcaagttaccgttgattaccgtt-tttcctatctt-------atatgttgt-ctttgtttctaagtgacgttta---tttgttta---atttacag

upper sequence: Vv12s0055g00710.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA15G05680.1 (Glycine max), 5'ss of exon 20
GTGGCATTTGTTGCAATCGGGGCAACGATGGTTGGTAGCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgtt---caaaattcatttttttatctcttttatttttcattgtggtgtccatgtattctgctatgcttctaattaacattctaccttcatttgctcatttacag
||||||||||||||||| || || || |||||||||||||| || || || || || |||||||| |||||  |||| ||||| ||||||   |||  | || ||  |||||  ||||  | |    | || || |  |||            |||||| |   |||     ||  |||    ||||||||
GTGGCATTTGTTGCAATAGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGATTATGTTAAGAAGGGAGATGAGgtttggcaagttacagttgattatcgtttttcctatcttatatgttgcctttgt------------ttctaagtggaatttg---tttgttta---atttacag

upper sequence: Vv12s0055g00710.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT5G57190.1 (Arabidopsis thaliana), 5'ss of exon 19
GTGGCATTTGTTGCAATCGGGGCAACGATGGTTGGTAGCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt-catttttttatctcttttatttttcattgtggtgtccatgtattctgctatgcttctaattaacattctaccttcatttgctcatttacag
|| || |||||||||||||| ||||| |||||||||||||| |  ||   || |||| | || ||  ||||| |||||||||| || ||    | || ||  |||| ||       | ||          | ||| |   |||   |   |||  |                                 
GTTGCTTTTGTTGCAATCGGTGCAACAATGGTTGGTAGCATAAATTTTGTTAGAAAGGAAGGAGAGCATGTGAAGAAAGGAGATGAAgtaagcagtttcaacttttcataagaaacacttcaagagaatatttcc-taacttcaatttatcttgcag--------------------------------

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|32247401|gb|CD713220.1|CD713220
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTNTGAAA-G
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGAAAAG
EST: gi|32269098|gb|CD718257.1|CD718257
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATNTCTCATTTGGTGGAAGTACTGTAATTTGTGTCNTTTGAAA-
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTC-TTTGAAAA
EST: gi|32249664|gb|CD715483.1|CD715483
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTTGAAA-
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTT-GAAAA
EST: gi|30328312|gb|CD011574.1|CD011574
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGAAAAG
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGAAAAG
EST: gi|30327654|gb|CD010916.1|CD010916
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTG-AAGTACTGTAATTTGTGTCTTTGAAAAG
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGAAAAG
EST: gi|32249812|gb|CD715631.1|CD715631
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGANAAG
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGAAAAG
EST: gi|32270392|gb|CD719551.1|CD719551
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTGGAAGTACTGT
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGT
EST: gi|30325758|gb|CD009020.1|CD009020
EST:     GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAG                         TTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGA
genomic: GCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaatt ... tcatttacagTTCGGATATTTCTCATTTGGTGGAAGTACTGTAATTTGTGTCTTTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCATTTGTTGCAATCGGGGCAACGATGGTTGGTAGCATCACCTTCACTAAAAAGAAGGGCGACTATGTGCAGAAAGGAGAAGAGgttcaaaattcatttttttatctcttttatttttcattgtggtgtccatgtattctgctatgcttctaattaacattctaccttcatttgctcatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA