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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccatcatgctgtatataatccattttccctttccatttcagaaaatattaatttgttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA

Basic information

species Vitis vinifera
transcript Vv10s0116g01480.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 9
-------ttccatcatgctgtatataatccattttccctttccatttcagaaaatattaatttgttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA
       ||| || ||| |  || |     |   |     ||| ||  ||    ||||||||| || ||||  | | |   |  | |  | |       |  | |||||| || || |||||||| |||||||||||||||||||  ||| |    |||||||| || || ||||| || |||||| | ||| | || 
tgtaaacttcaataatgat-catttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatcttacgattta------tgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTGTCAAG

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 9
-------ttccatcatgctgtatataatccattttccctttccatttcagaaaatattaatttgttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA
       ||| || ||| |  || |     |   |     ||| ||  ||    ||||||||| || ||||  | | |   |  | |  | |       |  | |||||| || || |||||||| |||||||||||||||||||  ||| |    |||||||| || || ||||| || |||||| | |||      
tgtaaacttcaataatgat-catttggcataccattatgatcctttgaaggctgtattaatttttttactctatctctgtatcttacgattta------tgatatagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTCAAATTGGGTCTTATGTCTTGCTTTG-----

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 3'ss of exon 6
----------------ttccatca---tgctgtatata-atccattttccctttccatttcagaaaat--atta-atttgttgactcactttttcgttgctgctgtgtgcttatttt----gtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA
                  || |||   || | | | || |||  || | |   ||| |||     | |  |||| | | ||    |   ||||   |      | ||    | ||||    || ||||||||| || ||||||||||| ||  | || || ||||| |||  ||| ||||||||||||||||||||||| ||||||||||||||||||
gtgagtaacagcttaaacccgtcaagttgatatgtctatatcagttatgcgagtccttttggtgcactgaattatactagtcagtttgattttatttgctaattatggagctcttttctgcgtgtagGACAAATTTGATGAAGCTCCGATCCCAATACAAGGATGCATTTTATGAAAAGCATGGAGTGAAGTTGGGGCTTATGTCTGGATTTATTAAA

upper sequence: Vv10s0116g01480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G55070.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------ttccatcatgctgtatataatccattttccctttccatt--tcagaaaatattaatttg---ttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA
                  |  |||| || ||||    | || ||  |||  | |   |  |    | ||||||       ||||     |||            | | |  ||    |||||| ||  | ||||||||||| ||| | || || |||||||||||||| ||||| ||||||||||||||||| |||||||| || ||||| 
gtgagttacagttgacaaccccatgttg-atatgtctctttatcattttgaaatgcccttagtgcactaattttaacccaactcttaagttcaccaacaaaactttccttcttcacgtagGACTAATCTGATGAAGCTCCGATCTCAGTACAAGGATGCTTTTCTTGAAAAGCACGGAGTGAAGTTGGGGCTTATGTCTGGTTTCATTAAG

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|34548183|gb|CF516415.1|CF516415
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
EST: gi|294964448|gb|GW838251.1|GW838251
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
EST: gi|71864219|gb|DT013274.1|DT013274
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
EST: gi|71861201|gb|DT010256.1|DT010256
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAA
EST: gi|71868220|gb|DT017275.1|DT017275
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
EST: gi|37189774|gb|CF609123.1|CF609123
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
EST: gi|110729049|gb|EE105210.1|EE105210
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
EST: gi|110718184|gb|EE094729.1|EE094729
EST:     GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATAT                         GACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA
genomic: GATTCTCAAAACACTTTTGCAATGCTGACCACATTCAATGAAGTTGATATgtaagttgta ... ttttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatattaatttgttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA
              gactcac  putative branch site (score: 2)
                                         cttatttt  putative PPT
                                          ttattttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccatcatgctgtatataatccattttccctttccatttcagaaaatattaatttgttgactcactttttcgttgctgctgtgtgcttattttgtttagGACAAACTTAATGAAGCTCCGTTCTGATTATAAAGATGCTTTTCTTGAGAAGCATGGAGTGAAGTTGGGGCTGATGTCTGGATTTATTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - -tcatgct
- - - - - - - - - - -ccatttt
- - - - - - - - - - - - - - ccctttc
- - - - - - - - - - - - - - - - - - - - -agaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctg