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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatcaatggttttggagaaatagttggaaatt...

Basic information

species Vitis vinifera
transcript Vv01s0010g01110.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 5'ss of exon 5
---TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaac----aaaatgttaattcatgactctat----atggtttattagttggt--tatgaatgggagcatgatcaatggttttggagaaa---tagttggaaatt-------------------------------------------------------------------------------
   |   | |||||||||||||| |||||||||||  |||| |||||||||||||| | |||| || |  |||||       || | ||||||||| ||||||||||| |     |    | ||| ||  ||    ||   ||    |||    |||   ||||  |||     |   |||   || |||     || |||   |  ||  ||  |                                                                               
TTTTCACTACTTGTTCTTCACATATATTGGTGGGTTCTGATATATCGGATGCTTGTGAGACAAATCAAGACAAGAAATG---TTGGAGATGATGTTCGATCTGgtaagctctgcccccttagaatcttgtttttgcacaggatgagcatgcaaaattgcatggtcttattttcagtcccatctgcattgggacaagacaaagtctgcttataacatgcattactccaaccaccattgtgagttgaaaattattttgagtttgctaccatctaaaactgttctgctttatgtgcag

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G315726_T02 (Zea mays), 5'ss of exon 3
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaa---caaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatcaatggtt---ttggagaaatagttggaaatt
|   | |||||||| ||||| ||||||||||| || ||||||||||||||||| || ||| | ||  | ||||| ||  || | |||||| |  ||||||||| |||        |   |  ||  |   | | | |||  |||| |  | ||     || ||   | |||  |     |||   ||   |  ||||||| |    
TCTCTACTTGTTCTACACATATATTGGTGGGTTTTAATGTATCGGATGCTTGTGAAGCAAATACAGTCTAGAGGGCACGTTGGCGATGATATACGATCTGgtaggttctccttttccttagattcttctgttattatatgaggttga--acttaaaattggataaaa-cattctttggagttaaattctggttatagttgaat---

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G444643_T01 (Zea mays), 5'ss of exon 6
---TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatcaat-------ggttttggagaaa---tagttggaaatt-------------------------------------------------------------------
   |   | |||||||| ||||| ||||||||||| || || |||||||||||||| | |||| || |  |||||       || | ||||||||| ||||||||||||      |    ||    ||    |  ||  |        |  ||  ||   ||||        |||| |       | || |||  |||   |||||  || |                                                                    
TTTTCACTACTTGTTCTCCACATATATTGGTGGGTTTTAATATATCGGATGCTTGTGAGACAAATCAAGACAAGAAATG---TTGGAGATGATGTTCGATCTGgtaagtcctgtcctgtctgaagttttggtatgctgcacacgagcatttttttttgaaaatgctgcgcaaatcagttttgtttgcttgtgggtaaaacttagttataattatgttctttcaacttgtgttgaggtgaaaaactttcttcgattttactttgccttgctttccatacag

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G170868_T01 (Zea mays), 5'ss of exon 5
---TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatg---actctatatg-gtttattagttggttatgaatgggagcatgatcaat-------ggttttggagaaa---tagttggaaatt-------------------------------
   |   | |||||||| ||||| ||||||||||| || || |||||||||||| | | |||| || |  |||||       || | ||||||||| |||||||||||       |    ||     |   |    ||  | | | |  | ||  ||  | |  |||  | ||| |||||||       | || |||| |||   |||||  || ||                               
TTTTCACTACTTGTTCTCCACATATATTGGTGGGTCTTAATATATCGGATGCTTCTGAGACAAATCAAGACAAGAAATG---TTGGAGATGATGTTCGATCTGgtaagccctgttctgtctgaagcctttggtatgctgcacacgagcatttttttttttgaaaaatttgtgca-gatcaattttgtttgcttgtggataaaacatagttataactttgaattttactttgccttgcttttcatacag

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G12080.1 (Glycine max), 5'ss of exon 5
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatcaatggttttggagaaatagttggaaatt--
|||||||||||| | || |||||||||||||||||||| ||||||||||||||||||||| |||||||||||||  || ||||||| |||||| ||||||||||||| |||      |  |     | |  |   ||||  | |    ||  |||     |  | | ||   ||   || |       |   | | |  |  
TGCTTGCTTGTTATGCATATTTATTGGTGGGTGTTGATATATCGGATGCTTGTTAAACAAATCCAAGCAAGAGGAAAAGTTAGTGAAGATGTTCGATCTGgtaagttgaaagatgtgttctgtgcaaggctttcgtatg--taaacttttcattaactgagcaaccttgtgaaaaatttgttcccctgtgcctagtatctgc

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G36370.1 (Glycine max), 5'ss of exon 5
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatcaatggttttggagaaatagttggaaatt---
|||||||||||| | || ||||||||||||||| |||| | ||||||||||||||||||| |||||||||||||  || ||||||| |||||| ||||||||||||| ||||    ||  |  | || | || | |   ||  | |      | |   |  | ||| |  | ||   |||       ||   | | |  |   
TGCTTGCTTGTTATGCATATTTATTGGTGGGTGCTGATATTTCGGATGCTTGTTAAACAAATCCAAGCAAGAGGAAAAGTTAGTGAAGATGTTCGATCTGgtaagttgaaaaatgcattctg-tgcaaggctttcttatgtaaactttccattgactga--gcagccttgtgaaaaatttgttccccatgcctagtatctgca

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G14060.1 (Glycine max), 5'ss of exon 9
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggt---ttattagttggttatg------aatgggagcatgat--caatggttt-tggagaaatagttggaaatt-------------------------------------------------------------------------------
| |||||| |||||||| || |||||||||||  |||||  | ||||||||||||||||| |||||| || |||  || ||||||| ||| |  ||||||||||| | ||      |  | |||  ||| || | || | |    | ||  |   |||||      |||   | | ||||    ||| |   |    |  |||       ||                                                                               
TTCTTGCTAGTTCTTCATATATATTGGTGGGTTCTGATGCTTAGGATGCTTGTTAAACAAATCCAAGAAAAAGGAAAAGTTAGTGAAGATATACGATCTGgtaagctgaatgatgcac-taaatatatgcctttctaagatgaactttttatgcattatgtcagaaaatattaacttgatgctgatgatccctatccatgtagcctcgggttttgaagtggccttactcaatagaaattttaacttgttatctgattgtaatctgtttcacatcacattttctttatgcag

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G14040.1 (Glycine max), 5'ss of exon 5
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggt---ttattagttggttatg------aatgggagcatgat--caatggttt-tggagaaatagttggaaatt-------------------------------------------------------------------------------
| |||||  |||||||| || |||||||||||  |||||  | ||||||||||||||||| |||||| || |||  || ||||||| ||| |  ||||||||||| | ||      |  | |||  ||| || | || | |    | ||  |   |||||      |||   | | ||||    ||| |   |    |  |||       ||                                                                               
TTCTTGCAAGTTCTTCATATATATTGGTGGGTTCTGATGCTTAGGATGCTTGTTAAACAAATCCAAGAAAAAGGAAAAGTTAGTGAAGATATCCGATCTGgtaagctgaatgatgcac-taaatatatgcctttctaagatgaactttttatgcattatgtcagaaaatattaacttgatgctgatgatccctatccatgtagcctcgggttttgaagtggccttactcaatagaaattttaacttgttatctgattgtaatctgtttcacatcacattttcgttatgcag

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G13580.2 (Arabidopsis thaliana), 5'ss of exon 5
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatga--tcaatggttttggagaaatagttggaaatt
|||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||| | ||||  |||||| | |||||||| ||||| ||||| |||||||||     |   |  |||     |  | |    |    ||       | |   | | || | | |  |   ||  |||   | |             
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTTTTGATGTATCGGATGCTTGTGAAACAAATACAAGATAGAGGCAAGCTTAGTGAAGATGTCAGATCAGgtaagtttggtttactgtaataaaaatcggtttt---cgcaccatcca--aatcaaagaagagatcttcaagtttgtgtctttctcgcag------------

upper sequence: Vv01s0010g01110.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G25540.1 (Arabidopsis thaliana), 5'ss of exon 6
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatca-atggttttggagaaatagttggaaatt
| |||||||||||||||||| |  |||||||| ||||| || ||||||||||| |||||||| ||||   ||||| | ||||| || ||||||||||| |||| |   || | ||| | ||| | ||  | | |    |    |  |      ||| |||      ||| |||  |  ||||| ||               
TTCTTGCTTGTTCTTCACATATTCTGGTGGGTTTTGATTTACCGGATGCTTGTGAAACAAGTGCAAGATCGAGGCAAGCTTAGCGAAGATGTTAGATCCGgtacgc--aataaaaactcttattacaatatttt----gagacaaaaacactctattaata-----atgttcatgtctttttgcag---------------

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|122691440|gb|EC977304.1|EC977304
EST:     TGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTG                         ACTCTGAAGATGAAGATGAACATGAAGATTGACCACGATACAAGATTTATG
genomic: TGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaa ... tttcatgtagACTCTGAAGATGAAGATGAACATGAAGATTGACCACGATACAAGATCTATG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTGCTTGTTCTTCACATTTATTGGTGGGTGTTGATGTATCGGATGCTTGTTAAACAAGTCCAAGCAAGAGGCCAACTTAGTGATGATGTTAGATCTGgtaagtttaaaacaaaatgttaattcatgactctatatggtttattagttggttatgaatgggagcatgatcaatggttttggagaaatagttggaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggaaa