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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttttttatttgcctatcctttaagattcagactcatctgttattttccctttcagttatgatttccccttatttatcatcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG

Basic information

species Vitis vinifera
transcript Vv16s0098g00320.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g50850.2 (Oryza sativa), 3'ss of exon 7
--attttttttatttgcctatcctt-taagattcagactcatctgttatt-ttccctttcagttatgatttc--cccttatttatcatcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG
  ||   ||  | |    | |  || | |  ||     || | |  |||| |||   ||  |||  | |||    || |||| ||     | |   ||  || ||||| || |||||||  ||| |||| |  |||||||||||||| |||||||||||| |||||||| |    |||
gtatgacttgcaatacgttgttattattaccttttttttcctgtcctattattcaactttcgttgggcttttgtaccctattgattg--gttttggtttttgccagGCTTTAGCTGCTCGTGGATTAAAAAGTGGTGGTACTGTTCAACAGCGTGCTGAGCGACTTTTCTTGTTGAAG

upper sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 6
---------------------------------attttttttat----ttgcctatc--ctttaagattcagactcatctgttat----tttccctttcagttatgatttccccttatttatcatcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG
                                 |||   || |     | ||   ||      || |||||   |||    | ||    ||     |  | | || || |    || ||  ||      | ||    ||| ||||| |||||||  | || || ||||| ||||||||||||||||| ||||| ||||| || ||||||||||||
gtaaattgtatgagtgtgtgtgtgagggtacatattccattaacaatgtagctggtcagtgcaaaaattcaccatcactaatcataaacttgataatatattgattatatttttttcttcttctctgctttttgatgtgatagGCACTGGCTGCGTTGGGGCTGAAGACTGGTGGTACTGTTCAGCAACGTGCAGAGAGGCTCTTCCTCACAAAG

upper sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G13290.1 (Glycine max), 3'ss of exon 6
----------------------------------at-tttttttatttgcctatcc------tttaagattcagactcatctgttattttcccttt-cagttatgatttccccttatttatcatcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG
                                  || ||   ||||   | || ||      | | | |||||   |||    | ||   |    |  | | || || |   ||| ||  ||      | ||  | ||| ||||| |||||||  | || || ||||| ||||||||||||||||| || || ||||| || ||||||||||||
gtaaaattgtatgagggtgcatgtgtgtcggtgcatattccattatcaacgtagccggtcagtgtgaaattcaccatcactaatcataaacttgatatattgattatattttctttttcttctctgctttttgacatgatagGCACTGGCTGCATTGGGGCTTAAGACTGGTGGTACTGTTCAGCAACGCGCAGAGAGGCTCTTCCTCACAAAG

upper sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 6
attttttttatttgcctatcctttaagattcagactcatc--tgttattttccctttcagttatgatttccccttatttat-catcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG
                       |||    || |||  |   ||||| | ||| |||     |  || | ||| || | ||   |  | | | | ||   ||||||||||  ||  ||||||| |||   |||||||||   ||||||||||| |||||||||||||| ||||||
----------------------gtaatgaccatactacttcatgttaatatcctttttga--agcatattcccctaatcatatgttctttgtatgccattcagGCATTGGGGGCATTAGGACTGAAGGTTGGTGGTACTCCGCAGCAGCGTGCCGAGAGACTTTTCCTGACAAAG

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|351040645|gb|FQ438189.1|FQ438189
EST:     ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAG                         GCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT
genomic: ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAGgtaaagtggt ... ttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT
EST: gi|351026899|gb|FQ436552.1|FQ436552
EST:     CAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAAATGTAAAAGGAG                         GCATTGGCTGCTCTAGGACTAAAGACAGGTGGGTACTGTTCAGCAGCGTGC
genomic: CAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAA-TGTTAAAGGAGgtaaagtggt ... ttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGG-TACTGTTCAGCAGCGTGC
EST: gi|351028525|gb|FQ444806.1|FQ444806
EST:     ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAG                         GCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT
genomic: ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAGgtaaagtggt ... ttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT
EST: gi|351021577|gb|FQ429681.1|FQ429681
EST:     ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAG                         GCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT
genomic: ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAGgtaaagtggt ... ttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT
EST: gi|161713801|gb|FC063789.1|FC063789
EST:     ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAG                         GCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGCGCT
genomic: ACAGTACAGTTGAAGAGGTGATGGAAGTGGGTCCTGAAATGTTAAAGGAGgtaaagtggt ... ttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccctttcagttatgatttccccttatttatcatcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG
                                    tcatatcttttcct  CT-rich tract
                          ttatttatcatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttttttatttgcctatcctttaagattcagactcatctgttattttccctttcagttatgatttccccttatttatcatcatatcttttcctgacagGCATTGGCTGCTCTAGGACTAAAGACAGGTGGTACTGTTCAGCAGCGTGCTGAGAGACTTTTCCTCACAAAG

- - - - - - tgcctat
- - - - - - - - - - - - - - - - -actcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccctt