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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaattatggggctaccatactatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG

Basic information

species Vitis vinifera
transcript Vv04s0023g00800.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 3'ss of exon 9
-agaaaattatggggctaccatactatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
 |     |||  |   |   |||   |||    ||  | |   | |     |    ||| |||  |   | |    |   || |  ||    |     ||||||||| || || ||||||||||||||||| || |||||| |||| |||||||  || ||||| ||| |  | || || |||
tatcttgtta-agaattctaataaattatcacaatcttttacataatagcatgcgtgttgtttacaattaatatcttagcttacaattttcttccaaacagTGACCGGCGTTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTGATACGTGAGAAGTTATCCGAACTGCAG

upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G028096_T04 (Zea mays), 3'ss of exon 10
--------------------------------------------agaaaattatggggctaccatactatat-gtggattctatc-tgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
                                               |  || |  ||||   |||   |||  |  | | | |  | || | |  |    ||| |  ||    ||  ||   ||| |||||| ||       ||||||||||||||| ||||||||||||||||| || |||||| |||| |||||||  || ||||| |   || | || || |||
gtgcgtgtttattatacatgtacatgtactattatcatgtgaaggatagtttttaaggctttaataacttatcataaactttgttatatgtatagttcacagtt-taccagcatagctaa---tttcccttttgatcca----cagTGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG

upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G028096_T02 (Zea mays), 3'ss of exon 9
------agaaaattatggggctaccatactatat-gtggattctatc-tgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
         |  || |  ||||   |||   |||  |  | | | |  | || | |  |    ||| |  ||    ||  ||   ||| |||||| ||       ||||||||||||||| ||||||||||||||||| || |||||| |||| |||||||  || ||||| |   || | || || |||
gtgaaggatagtttttaaggctttaataacttatcataaactttgttatatgtatagttcacagtt-taccagcatagctaa---tttcccttttgatcca----cagTGACCGTCGCTTGGCAGATCATTTTGGAGGGAAACTTCATATGGGTTATATGCTTATACGTGAGAGATTGTCTGAACTGCAG

upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G38430.1 (Glycine max), 3'ss of exon 9
-----agaaaattatggggctaccatactatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
     ||||| || |||||  |  || | |||| |  ||  |||          ||||||  | |||     |  | ||   |||   || |  | | ||| |||||| || || ||||| |||||||||||||| || |||||||| || |||||||| || ||||| ||| | || || ||||| 
tagttagaaatttttggggaaataatgccatatatcaata-tattgtcctgctgcttttgtatgtttt----gctttaatattttgatttgtattattattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATATGCAGATTCGTGAGAAGTTAGCCGAACTTCAA

upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------aga-aaattatggggctaccatactatatgtggat--tctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
           ||| |||| ||||  ||   | ||||||| |   |   | |||||| |    | |||||  || ||||       | ||||| | ||        |  || ||||| ||||| ||||| |||||||||||||| |||||||| ||||| || ||||  ||||| || ||  ||||||||||||||
gtgcctgttagagataaataatggaact-ttaaactatatctttgtcaccaatctgttatttgcatttggcaatgtcaaaa-----atctgttgtact--------gcctttagTGATCGTCGGTTAGCTGATCATTTTGGAGGGAAGCTTCACTTGGGTTACATGCTGATCCGCGACAAATTGGCAGAGCTTCAG

upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S402_41V6.1 (Physcomitrella patens), 3'ss of exon 9
------agaaaattatggggctaccatactatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
      |     ||  |  |     ||  | ||  ||   |  |  |        |   ||||   ||  | |      | ||  || ||  | |  |  |||||||||||||||||| || || ||||||||||| ||||| |||||||| |||||||| || ||||| ||||| |  ||  | | |
tcttctaatgggttcagaaggacttatcttttagatg--ctgcacttaatgctgccaagtggtgggtttcatgatt---agtgccttgctgctta-atactttcagTGACCGTCGCTTGGCGGACCATTTTGGAGGGAAGCTGCATTTGGGTTATATGCAGATTCGTGAGAAGCTCGTTGACTTGCGG

upper sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
agaaaattatggggctaccata---ctatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgat---ttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
      || |  ||||  || |   | |||| |   ||   |     | |   |  ||   | |    ||        ||  ||| ||||    | ||   ||||||||||||||| | || || ||||||||||| ||||| |||||||| || ||||| || || || ||||| |  ||  | |  
------ttttctggctttcaaaagacgatattttcttttactgccccacgtgttgctgccaagtagtgggtttcatgatgagttcttttttgcttaatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA

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|33403422|gb|CF209049.1|CF209049
EST:     AAGCTACGCGTATGTGACATTTGTGGAGCATTTTTGAGCGTTTATGATAG                         TGACCGTCGCTTAGCAGAT
genomic: AAGCTACGCGTATGTGACATTTGTGGAGCATTTTTGAGCGTTTATGATAGgtaaaatttt ... gtgatttcagTGACCGTCGCTTAGCAGAT
EST: gi|110702229|gb|EE080705.1|EE080705
EST:     AGCTACGCGTATGTGACATTTGTGGAGCATTTTTGAGCGTTTATGATAG                         TGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATAT
genomic: AGCTACGCGTATGTGACATTTGTGGAGCATTTTTGAGCGTTTATGATAGgtaaaatttt ... gtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG
                                ttttccttttcatgt  CT-rich tract
           ttatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaattatggggctaccatactatatgtggattctatctgtgaagaacttttggttatttcaagggagtgaactgttttccttttcatgtgatttcagTGACCGTCGCTTAGCAGATCATTTTGGAGGAAAGCTTCATTTGGGCTATATGCAAATCCGTGAAAAGCTGGCAGAGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
agaaaat
- - - - - - -gctacca
- - - - - - - - - - - - - - - - - - - - - -gaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggagtg