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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttcccatagtgttccaagacatgatacttgggagga...

Basic information

species Vitis vinifera
transcript Vv09s0054g00890.t01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 15
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgta-tgtttt---cctccttagcttttatttttct---attacacagctagatga-------gatagaaatgagccatttcccatagtgttccaagacatgatacttgggagga
 ||  |    ||||||    | ||||||||||| ||  | || || |||||||| ||||||||| |||| || ||||||||  |||||||||| ||||| ||| | ||||   |||  | |   |||| | | ||   ||| |||       |||        || ||| | | || |||| |||| |||   |   |                
TGAGCCGCACTATGAGAGGGAAGATCCAGATTTCATTGATATTAGAACAAAGGCACGTGAGGTGTTGCAGAGGGAAGATGATTTAAATGAAATAGTGCAGgtactattttgagccttgtgaatatttactctcctggaattccacgatggtttgacctgtcttattgaagtta-ccttttctcatactgtcgtatccctcc-------------

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 12
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttat-ttttctattacacagctagatgagatagaaatgagccatttcccatagtgttccaa-gacatgatacttgggagga----------------------------------------------------------------
 || || ||||||||| | | |||||||||||| ||  | || |||||||| || ||||||||| |||| || || || || ||||||||||||||||| ||| | ||| ||| | | |||||   ||| ||   ||| |     ||||  |   ||       || |  ||  |||  ||  | |||| |   |                                                                       
TGAGTCCTTTTATGAGAAGTTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTAAATGAAATTGTGCAGgtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaacttttt-ttccttattatgtggcattggcatgttttgtcatgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcag

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 15
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctcct--tagcttttattt--ttctattacacagctagatgagatagaaatgagccatttcccatagtgttccaagacatgatacttgggagga-----------------------------------------------------------------
 || |||||||| ||| ||| |||||||||||| ||  | || |||||||| || ||||||||| |||| || || || || || |||||||||||||| |||  |||| ||| |  |   ||| ||||  ||  | || | | |  ||||    |    |      |||   ||  ||   |   |  |  |    || || |                                                                 
TGAGTCTTTTTACGAGAAATTTGATCCAGATTTCATTGATATTAGGACAAAAGCACGTGAGGTGTTGCAGAGGGAGGACGATCTGAATGAAATTGTGCAGgtagattttgctcatattttttttcatttacttgcaataaaaaccatgatgtttcaacctttttttctttattatgttgcctcggcattttctggcaggcagcatggtaatgactaaaattttatcactagcactccattgtcttgattgtgacttcccgtgtgttcag

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 16
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttccca-tagtgttccaagacatgata-----cttgggagga---
 ||| | ||||||||||||| ||||||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| ||||||||||| || || ||| ||| |   | | |  |  || | |  ||         |||| ||        ||  | ||| | ||  |    ||||  || |      |||  |   |   
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATAAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttcttttattggtaatgattgtttgcta---------atgaaatgcccccatgctttctcctagtacgggattaagaattgttcagcttcttctgcaaatag

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 16
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttccca-tagtgttccaagacatgata-----cttgggagga---
 ||| | ||||||||||||| ||||||||||||||||||||| ||||||||||||||||| || |||||||| ||||||||||| ||||||||||| || || ||| ||| |   | | |  |  || | |  ||         |||| ||        ||  | ||| | ||  |    ||||  || |      |||  |   |   
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATCAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGGGAAGATGACCTGAATGAAATTGTTCAGgtgtgtgttcttttattggtaatgattgtttgcta---------atgaaatgtccccatgctttctcctagtacgggattaagatttgttcagcttcttctgcaaatag

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 16
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttcccatagtgttccaagacatgatacttgggagga
||||||||| |||||| | |  ||||||||||| ||||||||||||||||||||  | |||||| |||| || ||||| || || ||||||||||| || |||||| |  ||  |     | ||  | ||||||     |    ||||  |          ||   |  |||   ||  |||   |   ||         
GGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAGgtatgtatcacttatccttgtataagtatctattgtggtgaccaatgaactcttgtctcagcaaccctaatacattttgaaggggttgaacgataatctt

upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 16
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 16
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgta-------tgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttcccata-gtgttccaagacatgatacttgggagga-------------------------------------------------------------------------------
 |||  |||||||||| | | |||  | ||||||||    || || ||||| ||| | |||||| ||||  ||||||||||| |||||||||||||||| |||       ||   |       |  || |  |||  | ||  |||  |   || |  |||||||  |   ||   ||| || ||        | ||| |||                                                                                     
TGAAGGTTTTTATGAGAACTTTGACTCTGATTTTATTGGGATTAGAACAAAAGCTAGAGAGGTGTTGCAGCGAGAAGATGACTTAAATGAAATTGTGCAGgtaaggcaaatgcagtttgtgccacattgttctttcttgttttacatgtttctg-gtcagaaatgctcatatttttatatgttttttgtttatttatatttgtttcagcttttgtgaattccgtcgaatttatcttaactaacgtttttccatctggccattcctgtctaacctttctgggttacag

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|110720887|gb|EE097200.1|EE097200
EST:     AGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAA                         CTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAANATTACTCTAGA
genomic: AGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttc ... attactgcagCTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGA
EST: gi|110715176|gb|EE092929.1|EE092929
EST:     GGCTCGTGANGTGCTGNCCAAGAGA-GATGACCTAAATGAAATTGTGCAA                         CTTGTCNGAAAAGATGCTTTA
genomic: GGCTCGTGAGGTGCTG-CAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttc ... attactgcagCTTGTCGGAAAAGATGCTTTA
EST: gi|110707093|gb|EE083190.1|EE083190
EST:     AGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAA                         CTTGTCNGAAAA-ATGCTTT
genomic: AGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttc ... attactgcagCTTGTCGGAAAAGATGCTTT
EST: gi|37189190|gb|CF608539.1|CF608539
EST:     AGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAA                         CTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACT
genomic: AGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttc ... attactgcagCTTGTCGGAAAAGATGCTTTAGCTGAAACAGATAAAATTACTCTAGAGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATCTTTTTATGAGCAATATGATCCAGATTTTATCAACATCAGGACAAAGGCTCGTGAGGTGCTGCAAAGAGAAGATGACCTAAATGAAATTGTGCAAgtatgttttcctccttagcttttatttttctattacacagctagatgagatagaaatgagccatttcccatagtgttccaagacatgatacttgggagga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atagaaa