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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggttagaaaatgagcatgcatgctgattcccattgtaacaactttactgactcccatgcctgaattggtttaatagcttgaacatttcttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC

Basic information

species Vitis vinifera
transcript Vv09s0054g01090.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 3'ss of exon 17
tctggttagaaaatgagc-atgcatgctgattcccattgtaacaactttactgactccc---atgcctgaattggtttaatagcttgaacatttct--tcat---acagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC
          | |||||  || | |     ||| |  ||||  |  |||||   |  ||   ||||   |     |||  || |     |    |    |||   |||||| ||||| |||||||||||||| ||||| ||||||||||| ||    ||| | ||||| |||||||| ||||| ||||| || ||||     || ||  
-------ctgacatgagttatccttttcctttcactatgtatta--tttaccatcatccgagatgctaaataacattttttaccccccccccccccaaccatataacagGAGATCATTGGAGTCTTCAACAAAAACTGCATGATCAGCTACTCCGAGTATAGAAACATCTTCCCTATTTGGGCCCTTGGGGAGTACCGTCGCCGCGTCT

upper sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 17
---tctggttagaaaatgagcatgcatgctgattcccattgtaacaactttactgactcccatgcctgaattggtttaatagcttgaacatttcttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC
   |||  ||||  |  |   ||   || |         |||       || |    | |||| | | || |   | | ||   ||  |    |   |  ||||| ||||| ||||| |||||||||||||| |||||||| || ||    ||  ||||||  ||||| || |||||||| ||||| |||| ||  || || |
ttgtcttattagccagggttaatcgttggtcgcctggcatgttgtggtgttgcc--tttccattcgt-aactaactaactattgtgtccgccgcccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTACAGGAACACCTTCCCGATCTGGGCTCTGGGAGAGTACCGGTGCCGAGTCC

upper sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 17
-----------------------------------------------------tctggttagaaaatgagcatgcatgctgattccca--ttgtaacaactttactgactcccatgcctgaa---ttggtttaatagc----------ttgaacatttcttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC
                                                      ||| | |     |     ||   ||||  ||  |  | | ||  |  |   |  || |||||     |    ||||||                |||| | |  ||  || |||||||||||||| || ||||||| ||||||||||||||| || ||| | || |||   ||||| ||||| ||||| || || || |||| |       |  
gtacttgaatattggatgagtcggaataacgtagagccagaaatgacgtagtgactgttgaatttttatttctgtgggctgcgtctaaggtcggaattatctagttttctgccatggtcagagtgctggttttgcgctggtgttgatattgaccctaactgtatgcagGAAATCATGGGCGTATTCAACAGGAACTGTATGATCAGTTACTCTGCGTACCGGTGTATTTTTCCTATCTGGGCACTGGGTGAGTACCGGCAAAAATTGA

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|83275268|gb|DV938419.1|DV938419
EST:     CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAG                         GAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
genomic: CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAGgtaactctta ... cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
EST: gi|219555470|gb|FG984557.1|FG984557
EST:     CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAG                         GAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTGCATAT
genomic: CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAGgtaactctta ... cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
EST: gi|110415466|gb|EC981375.1|EC981375
EST:     CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAG                         GAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
genomic: CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAGgtaactctta ... cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
EST: gi|219555334|gb|FG984507.1|FG984507
EST:     CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAG                         GAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTGCATAT
genomic: CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAGgtaactctta ... cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
EST: gi|110701213|gb|EE078556.1|EE078556
EST:     CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAG                         GAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
genomic: CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAGgtaactctta ... cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
EST: gi|32459149|gb|CD800323.1|CD800323
EST:     CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAG                         GATATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT
genomic: CAAGGGTATTAATAAATTCCCAAATGAAGAATGGAGATTTCCCCCAGGAGgtaactctta ... cttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactgactcccatgcctgaattggtttaatagcttgaacatttcttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC
                                        catttcttc  CT-rich tract
                          tttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggttagaaaatgagcatgcatgctgattcccattgtaacaactttactgactcccatgcctgaattggtttaatagcttgaacatttcttcatacagGAAATCATGGGAGTCTTCAACAAGAACTGTATGATCAGCTATTCTACATATCGGAACATTTTCCCTATATGGGCTCTTGGAGAATACCAGTCTCGGGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - -agaaaat
- - - - - - - - gcatgca
- - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - -cccattg
- - - - - - - - - - - - - - - - - - - - - - - - - - actccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tagcttg