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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtatttgcatgatcacagaccaagactttatgtattcaggtttttgtttttgtttttcaaccatgaaagatctcttgatgtctattttttggagta...

Basic information

species Vitis vinifera
transcript Vv03s0038g02830.t01
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 25
ATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgta-----tttgcatgatcacagacc--aagactttatgtattcaggtttttgtttttgtttttcaaccatgaaagatctcttgatgtcta--------ttttttggagta------
||||||| ||||| ||||||||||||   |||||||||||||| || ||| | |  |||||||||||||| |||||| ||||||| | ||| || | || ||| ||      | |   |   |   ||||  |||  ||   | |   ||| |    ||   || ||| | | |||     |  | ||| |  |         || ||||| ||       
ATAGTGCGATCACTCTTGGGAGGCTTAGCTGGGTCTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGCAAGCATGGTGCAGTGCCTTGTGCACgtaagtgccccctctttttttccctggacccgaagggttagagaaggaaggatgggtttcaggtgttttatctatggtttgttgcatgacgaatggaacttgtttctttggtgtgaaccag

upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GRMZM5G869572_T01 (Zea mays), 5'ss of exon 5
ATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtatttgcatgatcacagaccaagactttatgtattcaggtttttgtttttgtttttcaaccatgaaagatctcttgatgtctattttttggagta
| || || ||||| ||||||||||||   ||||| |||||||| || ||| | |  |||||||||||||| |||||| ||||||| |  || || | |||||| |      | |  ||      |     |      || |      ||       ||     || |    |  |   ||| |   | |  |   |    
ACAGCGCGATCACTCTTGGGAGGCTTAGCTGGGTGTGTCCAGACATCGTGGCCCCTCATATGGAGCATTTCATGCAAGCATGGTGCAAGGCGTTGTGCATgtaagggccccccttttctggagtcttttttaagcacatcccaagagttagaga-attgcatgacgaatggaacttgtttgtttggtgtgatccag----

upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GLYMA10G42960.1 (Glycine max), 5'ss of exon 25
ATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgt------atttgcatgatc-acagaccaagactttatgtattcaggtttttgtttttgtttttcaaccatgaaagatctcttgatgtctattttttggagta----
||||||| || || || ||||||||||| ||||||||||| ||  |||| ||||  |||||||||||||| |||||||| ||||| |||||||| || ||||  ||      |  |   || |  |   |  |     |||   | | ||    | |    ||| |||           | |||||| | || |  |  |   || |    
ATAGTGCAATAACACTGGGGAGGCTTGCATGGGTCTGTCCGGAGCTTGTATCACCACATATGGAGCATTTCATGCAATCTTGGTGCACTGCTTTGTCAATgttagttgtagcacctatgtgttttatttagtagcgacttacacaatgagcacatagcaaatgtcttt----------ggttctcttca-gtttgctgctataagaaaatg

upper sequence: Vv03s0038g02830.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GLYMA20G24040.1 (Glycine max), 5'ss of exon 25
ATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtatttgcatgatcacagaccaagactttatgtattcaggttttt----gtttttgtttttcaaccatgaaagatctcttgatgtctattttttggagta----
||||||| || ||  | ||||||||||| ||||||||||| ||  |||| ||||  |||||||||||||| |||||||| ||||| |||||||| || ||||| ||  |      | |||  |       ||||| || | | |  ||      |       |  |||  ||    | |    |   || |  |  |   || |    
ATAGTGCAATAACATTGGGGAGGCTTGCATGGGTCTGTCCGGAGCTTGTATCACCACATATGGAGCATTTCATGCAATCTTGGTGCACTGCTTTGTCAATgtaagttgt------accacttat--gtgttttatatagtaatgacttccacaatgagcacataacaaatatatttggttctctttagtttgctgctataagaaaatg

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|71885305|gb|DT034360.1|DT034360
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
EST: gi|71882863|gb|DT031918.1|DT031918
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
EST: gi|71887036|gb|DT036091.1|DT036091
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
EST: gi|71885604|gb|DT034659.1|DT034659
EST:     TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCAT                         GATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT
genomic: TCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtattt ... tttgtggcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGTGCCATCACCCTTGGGAGGCTTGCTTGGGTCTGTCCAGAAATTGTGTCACTGCATATGGAGCATTTTATGCAATCATGGTGTACTGCTTTATCCATgtacgtatttgcatgatcacagaccaagactttatgtattcaggtttttgtttttgtttttcaaccatgaaagatctcttgatgtctattttttggagta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaagat