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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATGGGATAAAAGGTCCGGAGTCTATTGCTGATCACATGTACCGCATGGCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttgtttgaacgtatcactgcttgtgctttttgtttttaaacatattttcaggttattctcggtgatatttctgcttgtttaagtattaactag...

Basic information

species Vitis vinifera
transcript Vv01s0011g02430.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g45390.2 (Oryza sativa), 5'ss of exon 2
ATAATGGGATAAAAGGTCCGGAGTCTATTGCTGATCACATGTACCGCATGGCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttgga------cttgtttgaa----cgtatcact-------gcttgtgctttttgtttttaaacatattttcaggttattctcggtgatatttctgcttgtttaag--tattaactag--------------------------------------------------------
|  || | ||||| ||||| |||||||||||||||||||||||||| |||||  | ||||| |||||||| |||||||| | || |||  |  | |||||||  |       ||| ||  ||    | || || |       ||   | | | |  | |||   ||| |  | |  | |||  |    | ||  | | |  || | |  |  |  |||                                                         
ACCATAGCATAAAGGGTCCTGAGTCTATTGCTGATCACATGTACCGTATGGCCCTTATGGCTTTGATTGCCGGTGACCTACCTGCTGTAGATCGAGAAAGgtccgtgtttttcttattcaaatttccatagcattaaaaaatgccctttcgtctgttctttgttcatctagttaattgatta-caacaaaataccagatgtttcaggcttcctttctaaattagtcattagttatttacttgtttgtgatgacatatttattttacctaaaacag

upper sequence: Vv01s0011g02430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G088397_T01 (Zea mays), 5'ss of exon 2
ATAATGGGATAAAAGGTCCGGAGTCTATTGCTGATCACATGTACCGCATGGCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgt--------tggacttgtttgaacgtatcactgctt--gtgctttttgtttttaaacatattttcaggttattctcggtgatatttctgcttgtttaagtattaactag
|  || | || || || || ||||| |||||||||||||||||||| ||||| ||||||||  ||||||||||||| || | || |||| |  | |||||||        |  | ||  |    ||  | | || ||   |    |||    ||   ||||| ||    || | || |||| |     |  || |||||  |        
ACCATAGCATCAAGGGCCCTGAGTCCATTGCTGATCACATGTACCGAATGGCCTTGATGGCTCTGATTGCTGGTGATCTGCCTGCTGTGGATCGAGAAAGgtccatctcttcaaattaatctttcgctttattgtttcgttatgctttagcctttgtcatatcttagttttctgcttggtgttgaccatcattctttaatcag-------

upper sequence: Vv01s0011g02430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G14300.1 (Glycine max), 5'ss of exon 2
ATAATGGGATAAAAGGTCCGGAGTCTATTGCTGATCACATGTACCGCATGGCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttgtttgaacgtatcactgcttgtgctttttgtttttaaacatattttcaggttattctcggtgatatttctgcttgtttaagtattaactag
|| |||||||||||||| | || || |||||||| || |||||||||||||| || ||||| ||||||||||| ||  |||  ||  ||||  | ||||||||  || |       |   |||   |||||  | |   || |||      |  ||    | |||  | || |  ||  | |||||| | ||| |  |  
ATCATGGGATAAAAGGTGCTGAATCGATTGCTGACCATATGTACCGCATGGCTTTAATGGCATTGATTGCTGGCGATGTTCCAGGATTGAATCGAGAAAGgtttcacattgaaattctcttcatctcttgttatatgaattcttatgatgctcgtctctgttttcgtgttggttctttggtttgttttattatgagatta

upper sequence: Vv01s0011g02430.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S286_37V6.1 (Physcomitrella patens), 5'ss of exon 1
ATAATGGGATAAAAGGTCCGGAGTCTATTGCTGATCACATGTACCGCATGGCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttgtttgaacgtatcactgcttgtgctttttgtttttaaacatattttcaggttattctcggtgatatttctgcttgtttaagtattaactag---------
|| ||||| | || |   |||| |||||||||||||||||||||||||||||| |||||||  | ||  | || ||| | |  || ||||| |  || |||| ||  |  | | |   | ||| || | ||    ||        | ||| | | ||||   |  |   | | ||||||  | || | ||  | || |           
ATCATGGGGTGAAGGAGTCGGAATCTATTGCTGATCACATGTACCGCATGGCAGTGATGGCTATCATCTCAGGAGACTTACCAGGCGTGAATAAAGACAGgtgggtttcatctaac--tttcattgatggt----ttcaggccccagcatttgtacagggggtgatgaat-agatttct--tggtgtcagcttcaattcatcctaaaga

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|351054374|gb|FQ450457.1|FQ450457
EST:     GCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAG                         GTGTATTAAGATAGCAATTGTGCATGATATTGCAGAAG
genomic: GCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttg ... atttaaacagGTGTATTAAGATAGCAATTGTGCATGATATTGCAGAAG
EST: gi|110390616|gb|EC955535.1|EC955535
EST:     GCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAG                         GTGTATTAAGATAGCAATTGTGCATGATATTGCAGAAG
genomic: GCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttg ... atttaaacagGTGTATTAAGATAGCAATTGTGCATGATATTGCAGAAG
EST: gi|56408738|gb|CX016990.1|CX016990
EST:     GCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAG                         GTGTATTAAGATAGCAATTGTGCATGATATTGCAGAAG
genomic: GCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttg ... atttaaacagGTGTATTAAGATAGCAATTGTGCATGATATTGCAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATGGGATAAAAGGTCCGGAGTCTATTGCTGATCACATGTACCGCATGGCATTGATGGCGTTGATTGCTGGTGACCTTCATGGTGTGAACAGGGAAAGgttggacttgtttgaacgtatcactgcttgtgctttttgtttttaaacatattttcaggttattctcggtgatatttctgcttgtttaagtattaactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacata