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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacaatgcattatttatgtttaaccattggtgcttgtcctatattacctagcaaattatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG

Basic information

species Vitis vinifera
transcript Vv02s0012g00140.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G065105_T02 (Zea mays), 3'ss of exon 1
aaaacaatgcattatttatgtttaaccattggtgcttgtcctatattacc---------tagcaaattatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG
         |  || ||   |||   | |||| |      | | |||            ||||| ||    | |  |    | |         ||   | | | | ||| ||||||||||||||| ||||||||||||| ||  | |   | |  ||||||||||| ||||||||||| |  |||||| |||| || |||||
---------cgctagttggatttggactttggagaccagaccagattgttgacctctggtagcacataggatgcgatcgactgacgcttcccgcttgatttgtctgcagAAATGGGTTCCAGAAGCTGGAGAAGATCAAGGATGCCAACCGCCGCAGCAGGCAGCTTGAAGAGCTTACTGATAAGATGCGAGACTGCAAGAG

upper sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G065105_T03 (Zea mays), 3'ss of exon 1
aaaacaatgcattatttatgtttaaccattggtgcttgtcctatattacc---------tagcaaattatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG-------
         |  || ||   |||   | |||| |      | | |||            ||||| ||    | |  |    | |         ||   | | | | ||| ||||||||||||||| ||||||||||||| ||  | |   | |  ||||||||||| ||||||||||| |  |||||| |||| || |||||       
---------cgctagttggatttggactttggagaccagaccagattgttgacctctggtagcacataggatgcgatcgactgacgcttcccgcttgatttgtctgcagAAATGGGTTCCAGAAGCTGGAGAAGATCAAGGATGCCAACCGCCGCAGCAGGCAGCTTGAAGAGCTTACTGATAAGATGCGAGACTGCAAGAGGTTGCTC

upper sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G15990.1 (Glycine max), 3'ss of exon 1
---aaaac---aatgcattatttatgtttaaccattg-gtgcttgtcctatattacctagcaa----attatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG
   | |||   ||     |  | ||  | |  ||||  ||| ||     || || | |  | |     || | |||||        | |||| || | ||| |  || ||| ||||| || ||||||||||||||||| || ||  ||| ||| |||||||||||| ||||||| || ||||  ||  || |||| |||||  |
gtcagaaccttaaccttcttctcattctcattcatttcgtgttttgatgatgttccgttcccacgttgttgttttcttctgatcggtgtaatgttgt-tgt-tggttgcagAAATGGATTTCAGAAGTTGGAGAAGATTAAGGATTCGAATAGACAGAGCAGGCAGTTGGAAGACCTCACGGAAAAATTGCGAGAATGTAAACG

upper sequence: Vv02s0012g00140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G35190.1 (Arabidopsis thaliana), 3'ss of exon 1
aaaacaatgcattatttatgtttaaccattggtgcttgtcctatattacctagcaaat-tatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG
   | |||| ||   |    | || |  ||    ||   | | | | |  | | |  | | |||   | |   |  | | || || | ||| ||| ||||| ||||| ||||||||| ||||||||||||||||  | | ||||||||| |||||||||||||| || || |  || ||| | || ||||||||
gtgagaatgaatctctc---tctagcgtttt---ctctccatttgtgatttggtatttgtgtctatataataatgttttgatgtttt-tgt-tttctacagAAATGGATTCCAGAAGCTGGAGAAGATCAAAGATGCTAATAGGCAGAGTAGGCAGCTGGAAGAACTCACTGACAAAATGCGTGACTGTAAGAG

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|71861697|gb|DT010752.1|DT010752
EST:     GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATC                         TAATGGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCA
genomic: GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATCgtaaggaatc ... atttttacagTAATGGG-TTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCA
EST: gi|71857121|gb|DT006176.1|DT006176
EST:     GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATC                         TAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAG
genomic: GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATCgtaaggaatc ... atttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAG
EST: gi|71858665|gb|DT007720.1|DT007720
EST:     GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATC                         TAATGGGTTCCAGAAGTTGGAGAAGATCAAAGAC
genomic: GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATCgtaaggaatc ... atttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGAC
EST: gi|71858551|gb|DT007606.1|DT007606
EST:     GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATC                         TAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAG
genomic: GAGCTGGCGGAGATCGATGGACAAATTAGTGACATTTTCCGCGCGTTATCgtaaggaatc ... atttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacctagcaaattatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG
                             atctaat  putative branch site (score: 3)
                                            tattttt  putative PPT
                           taatctaattttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacaatgcattatttatgtttaaccattggtgcttgtcctatattacctagcaaattatcttctttaaggtaatctaattttctatgtatttttacagTAATGGGTTCCAGAAGTTGGAGAAGATCAAAGACACGAGTAGGCAGAGCAGGCAGCTGGAAGAGCTTACGGGGAAGATGAGAGAGTGTAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
aaaacaa
- - - - - - - - - - - - - - - -gtgcttg
- - - - - - - - - - - - - - - - - - - - - - - - cctagca