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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgctcactctaaactttctggaaatctatgctgatgc...

Basic information

species Vitis vinifera
transcript Vv01s0026g00340.t01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 17
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgc--tcactctaaactt-tctggaaatctatgctgatgc---
 ||||||||||| ||||| || ||||||||||| ||||| || || || ||||| ||||||||| | || ||       ||   |  ||||||     ||||   |  | |   || |  | ||  || |    |   || ||  |   || | |  | ||  ||   | |    |||||| | | ||  | ||  |   | |   
TCTTTTGGAGCATTACAATGGTAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGCTCGGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtgaat--ggttcttgtatctataaaaact----gacttgacttcatagttctctgttgtggctgacattaagagaaacttctgttgagttataatccacttcgtg

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GRMZM2G137615_T01 (Zea mays), 5'ss of exon 6
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgctcactctaaactttctggaaatctatgctgatgc----
 ||||||||||| ||||| || ||||||||||| ||||| || || || ||||| ||||||||  | || ||       ||   |  ||||||     |||||  |   |  |||  | ||   | ||       |  |||  |    |  ||    |   || ||   |  | || ||     || || ||| |  |      
TCTTTTGGAGCATTACAATGGCAAATGGCCCTTATGGCTAAGCCCTCGCCAGGCCATTGTTTGTTCAGTATCTTCTGGTTCAGTGGAATATGCGAAACAGgtaaatggtccttatatatatcggggaaaa---aatgttgtgcaatcaagctttccgtgcaatcgccgccaatcaaattatcaaaagtc-atgatattttttta

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA01G03930.1 (Glycine max), 5'ss of exon 16
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgta-gttttgctgtatgcaaatttagcaatttctggtaatgtctataatatt-ttataatttgattgct---cactctaaactttctggaaatctatgctgatgc
|||||| |||||||||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||||||||| || || || ||  | ||||||||  |||||  |    ||| ||   |   |  || | | ||||| | | | |  |||   ||| ||     || |    |||    |   | || |||    |  | ||  
ACTTTTAGAGCACTACAAGGGTAAATGGCCTTTCTGGCTCAGTCCTCGTCAAGCGATTGTATGCCCTGTGTCTGAAAAGTCACAATCTTATGCACTACAGgtacatagctctgaattttaggctt-cattctatggta-tatttgtcttataactatgatacagatgatgtgtactgcgtaacatgtgaaaacactt-ttaat--

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: GLYMA02G03750.1 (Glycine max), 5'ss of exon 16
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgta-gttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgctcactctaaactttctggaaatc-tatgctgatgc--
|||||| |||||||||||||| |||||||| |||||||| ||||| ||||| || ||||| ||||||||||| || || || ||  | |||||| |  |||||  |    ||| ||   | | |  || | | ||||| |   | |  |||   | ||||  ||    ||    |    | ||| | ||| | ||   |  |  
ACTTTTAGAGCACTACAAGGGTAAATGGCCTTTCTGGCTCAGTCCTCGTCAAGCAATTGTATGCCCTGTGTCTGAAAAGTCACAAGCTTATGCATTACAGgtacatagctctgaattttagtctt-cattctatggta-tacttgtcttata--acaattaaatgatacagatgatgtgtactgcatatcatgtgacaacactt

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: AT5G26830.1 (Arabidopsis thaliana), 5'ss of exon 17
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgctcactctaaactttctggaaatctatgctgatgc-----
| | |||||||| ||||| || ||||||||||||||| ||||||| || ||||| || ||||| ||| | |||||||||||||||| |||||||   |||||   |||  ||  ||    | ||    |||   | |     | |  |  ||    | ||  ||||    ||||| || |   |   | | |  |||  |     
ATTGTTGGAGCATTACAAAGGAAAATGGCCCTTCTGGATTAGTCCGCGACAGGCCATAGTTTGTCCTATATCAGAGAAATCTCAGCAATATGCAGAAAAGgttacttttgtggctgttgctgtactcttttactg-agcacatgtggttcttatcgacttatttgcagtgtctaatctct---ggtttttcttttgacacaacag

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 17
lower sequence: PP1S400_36V6.1 (Physcomitrella patens), 5'ss of exon 17
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgt--agttttgctgtatg-----------caaatttagcaatt-tctggtaatgtctataatatttta-taatttgattgc--tcactctaaac---tttctggaaatctatgctgatgc-------------
 ||  |||| |||||    ||||||||||| || ||||| ||||||||||||   || |||||||| || ||||||||||    ||  |||||  |  ||||    | ||||  |||            |||| | | || |  | | || |||    |  | ||||   |||||||   |  |||   |   |    |  | |   |   | ||||||              
TCTGCTGGAACACTATGCAGGGAAATGGCCTTTTTGGCTGAGTCCACGTCAGTGTATCGTTTGCCCGGTATCAGAGAAATTCACGCATTATGCGGTGGAGgtccgttcttgcattatctcacctgggatcaaaatgatcattagtttagttatgaagttcgtgttttggcaatttgacaacaatcatcgtcgccgcactcatcggtgtgacttctgatggggtgttggtacag

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|32268540|gb|CD717699.1|CD717699
EST:     AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAG                         GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCG
genomic: AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgc ... attctcatagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCG
EST: gi|32249386|gb|CD715205.1|CD715205
EST:     AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAG                         GTAAGGGATCAGATTCATCAAGCT
genomic: AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgc ... attctcatagGTAAGGGATCAGATTCATCAAGCT
EST: gi|22011637|gb|BQ796671.1|BQ796671
EST:     AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAG                         GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACT
genomic: AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgc ... attctcatagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACT
EST: gi|110360907|gb|EC924350.1|EC924350
EST:     AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAG                         GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACT
genomic: AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgc ... attctcatagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACT
EST: gi|22011184|gb|BQ796218.1|BQ796218
EST:     AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAG                         GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACT
genomic: AGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgc ... attctcatagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTCGATACAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTTTGGAGCACTACAAGGGGAAATGGCCCTTCTGGCTTAGTCCACGTCAGGCGATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTAAGgtagttttgctgtatgcaaatttagcaatttctggtaatgtctataatattttataatttgattgctcactctaaactttctggaaatctatgctgatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggaaat