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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttaaactaccttttttttcgacataaatagtgtaaatttaaggatttttcctagtgggagggctaacatacatagctcaattgatggacggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATTGACGGGAACAAAGAAATGATCGCATTTGGAATGATGAATCTCGTGGGCT

Basic information

species Vitis vinifera
transcript Vv05s0020g03970.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03970.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G154211_T01 (Zea mays), 3'ss of exon 6
----------------------agttaaactaccttttttttcg-----acataaatagtgtaaatttaaggatttttcctagtgggagggctaacatacatagctcaattgatggacggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATTGACGGGAACAAAGAAATGATCGCATTTGGAATGATGAATCTCGTGGGCT
                      |       | | |  ||| ||      ||   |     ||||   |  ||  ||   |  |||  |         | ||  ||     ||   |   | || ||||||||  |||| ||||| || |||||||||||||  |||||||| ||||| ||||| ||||| || ||||||||  | || | ||||||  || ||||||
gtaaggctcctttaatcaccacaccctgcttccttcctttctcccagtcactcgatcgccgtaagactgggggattaaac--gtgtcactcactgtgtgcaatgcgtgcgtgcgtgcgtgcgtgcagGAAGGCATCGCCGTGGGGAGGAGCTTCGCCATGTTCAAGAACTACCACATCGACGGCAACAAGGAGATGATCGCGATCGGGACGATGAACGTCCTGGGCT

upper sequence: Vv05s0020g03970.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ09164 (Selaginella moellendorffii), 3'ss of exon 7
agttaaactaccttttttttcgacataaatagtgtaaatttaaggatttttcctagtgggagggctaacata---catagctcaattgatggacggggt--acagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATTGACGGGAACAAAGAAATGATCGCATTTGGAATGATGAATCTCGTGGGCT
                                                 | | ||       ||||| ||     ||| | | | |  |  |   | ||  ||||||||   | ||||||||| |||  || ||   |   ||||||||||| || ||||| ||||| || |||||||| ||||||||| ||||  |   ||| |
------------------------------------------------gtacgtaccaaagtggctatcacggatcatggttgactgaagagtttgtgtccacagGAAGCTATTGCAGTGGGACGAACATTTGCATCGATCAAGAACTATCATATCGACGGCAACAAGGAGATGATCGCTTTTGGAATGGTGAACATGACGGGGT

upper sequence: Vv05s0020g03970.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ07197 (Selaginella moellendorffii), 3'ss of exon 7
agttaaactaccttttttttcgacataaatagtgtaaatttaaggatttttcctagtgggagggctaacata---catagctcaattgatggacggggt--acagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATTGACGGGAACAAAGAAATGATCGCATTTGGAATGATGAATCTCGTGGGCT
                                                 | | ||       ||||| ||     ||| | | | |  |  |   | ||  ||||||||   | || |||||| |||  || ||   |   ||||||||||| || ||||| ||||| || |||||||| ||||||||| ||||  |   ||| |
------------------------------------------------gtacgtaccaaagtggctatcacggatcatggttgactgaagagtttgtgtccacagGAAGCTATTGCGGTGGGACGAACATTTGCATCGATCAAGAACTATCATATCGACGGCAACAAGGAGATGATCGCTTTTGGAATGGTGAACATGACGGGGT

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|351028995|gb|FQ434996.1|FQ434996
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|351044188|gb|FQ443612.1|FQ443612
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|351016423|gb|FQ423850.1|FQ423850
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|110712914|gb|EE088377.1|EE088377
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349825477|gb|FQ419394.1|FQ419394
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349830794|gb|FQ417092.1|FQ417092
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349830077|gb|FQ420337.1|FQ420337
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349828704|gb|FQ418439.1|FQ418439
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349808259|gb|FQ403446.1|FQ403446
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|351016929|gb|FQ424356.1|FQ424356
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|351048769|gb|FQ449637.1|FQ449637
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGGAGCTTCCCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349816868|gb|FQ399736.1|FQ399736
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|349811423|gb|FQ409419.1|FQ409419
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|294964695|gb|GW838498.1|GW838498
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT
EST: gi|37183632|gb|CF602986.1|CF602986
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCAC
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCAC
EST: gi|352786783|gb|FQ481158.1|FQ481158
EST:     TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCT                         GAAGGAGTCGCAGTGGGAAGGAGCTTCGCCATGTATAAGAACTATCACATT
genomic: TGATGACAGCCATTAAAGCAGGAGCCACCATTGGGATCATATCCCTAGCTgtaagttcta ... cggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcctagtgggagggctaacatacatagctcaattgatggacggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATTGACGGGAACAAAGAAATGATCGCATTTGGAATGATGAATCTCGTGGGCT
                    taacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttaaactaccttttttttcgacataaatagtgtaaatttaaggatttttcctagtgggagggctaacatacatagctcaattgatggacggggtacagGAAGGAGTCGCAGTGGGAAGAAGCTTCGCCATGTATAAGAACTATCACATTGACGGGAACAAAGAAATGATCGCATTTGGAATGATGAATCTCGTGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgga