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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag

Basic information

species Arabidopsis thaliana
transcript AT2G25760.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctg-gtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag
|||||||||||| || ||| | || || ||||||||||||| ||| ||||| || || ||||| || ||||| |||||||| |||||| | |||||||||||| |  ||||   | |  || |    ||      | | |||| | ||   ||||     | | | | | |   ||  |  | |   | |||
GGATCAGGCTGCATTCGTTTTAAGCGTCCCAAGAAGGAAGCCTACAGATGAAACTCAAGAGACGCTGAGAACATCTGCTTTCCCTAGTCAACATGTCAAGgttcgtctgcttcatatactagtaacgtacttggcagtttttgccgttagtacttt----gctctgacagagtgatgcttgtctcgttccag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag
 || ||||  || ||  |  | ||  | || ||||| |||| || |||||| ||||||||||| || ||||| |||||||||||| |  | ||||| |||||     | |     |||| | ||||  |  |     | |   | |  ||| |        | | ||| ||||||||              
TGACCAGGTGGCTTTGATCTTGAGCATACCTAGAAGAAAGCCTAACGATGAAACACAGGAGACACTGAGAACATCTGCTTTTCCTGGCCAGCATGTAAAGgtgactataccttcttcttgtgccttgtttga-----actccacataacaaat-----aaatctgataaatctatttgcag----------

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag-----------
||| ||||| |||||| |  | ||  | ||||| || |||| ||| ||||| ||||||||||| || ||||| ||||||||||||||  | ||||| |||||  |||| |   | ||| | |||||| || ||    |||| |    |   ||   |  || ||  | ||| |||| ||  |  |   ||            
GGACCAGGCGGCCTTTATCTTGAGCATACCAAGGAGAAAGCCTACTGATGAAACACAGGAGACCCTGAGAACATCTGCTTTTCCTAGCCAGCATGTGAAGgta-gcttacc--tttctcactcctttttcgatgtgaattttgtgagct--ctaggtaaggggttttgtatttattatacctcctgatcaatctatttacag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G158177_T01 (Zea mays), 5'ss of exon 8
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaat-atatctattttat------tttttctgcag
||| ||||| |||||| |  | ||  | ||||| || |||| ||  ||||| ||||||||||| |||||||| ||||| ||||||||  | ||||| |||||    |  |   | ||   ||  ||    |   ||| | ||   | |     |   |   |||| | ||  | |  ||||      | | | | |||
GGACCAGGCAGCCTTTATCTTGAGCATTCCAAGGAGAAAGCCTAGTGATGAAACACAGGAGACCCTTAGAACATCTGCGTTTCCTAGCCAGCATGTGAAGgtagcttgacctttgtcactttttttagatctgaattttgtgagctccaggtatagggttttgtatttattcccaccttatgatcaatctatttacag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag
|||||| ||||| |||||||||||||| |||||||| || |   | ||||| || |||||||| ||  | || |||||||||||||||| ||||||||||||    | |    |||  | ||||||||| ||||   |||      ||  || | ||       || || |  ||||| ||||| ||||||
GGATCAAGCTGCTTTTGTTCTTAGTGTCCCAAGAAGAAAACCAGCTGATGAAACTCAGGAGACACTCCGCACATCTGCTTTTCCTAGTACTCATGTCAAGgtaaa-tagtgcatctgattttcctttattcatttccattccatgatcacacatgtt-------aacat-ttgattttttttttcctgcag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgc-ttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag
||| || ||||| |||||||||||||| |||||||| || |   | ||||| || |||||||| ||  | || |||||||||||| ||| ||||||||||||   | ||||   |||  | ||||||||| |||| | |||      ||  || |  |    | | || |      ||| ||| |  |||||
GGACCAAGCTGCTTTTGTTCTTAGTGTCCCAAGAAGAAAACCAGCTGATGAAACTCAGGAGACACTCCGCACATCTGCTTTTCCTGGTACTCATGTCAAGgtaaacattgc--atctgattttcctttattcattgtcattccatgatcgcacatgctaacatttgattt------tttttttctcttgcag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgc-ttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag
||| || ||||| |||||||||||||| |||||||| || |   | ||||| || |||||||| ||  | || |||||||||||| ||| ||||||||||||   | ||||   |||  | ||||||||| ||||   |||      ||  || |  |    | | ||       |||| ||| |  |||||
GGACCAAGCTGCTTTTGTTCTTAGTGTCCCAAGAAGAAAACCAGCTGATGAAACTCAGGAGACACTCCGCACATCTGCTTTTCCTGGTACTCATGTCAAGgtaaacattgc--atctgattttcctttattcattgccattccttgatcacacatgctaacatttgat-------ttttttttctcttgcag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgt------------ttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttgg----ggtgtaatatatctattttattttttctgcag---------------
||| |||||||| |||||||||||||| |||||||| || | | | ||||| ||||| ||||| || ||||| |||||||||||||| |  |||||||||||            || ||| ||  ||| || ||   || ||  || |  |||| || | |    |||| |    ||| |    | || | |||| | ||| |  |                
GGACCAGGCTGCTTTTGTTCTTAGTGTACCAAGAAGAAAACCTGCAGATGAAACACAAGAGACGCTCAGAACTTCTGCTTTTCCTAGCACACATGTCAAGgtggattatttgcattactttcttttcttttcttttcttttcttttttcttttgcctgttccttgtcttagaattggtttttgttttcaaatttaatatttatatatggtggtttcttacag

upper sequence: AT2G25760.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 15
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgt------ttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatat--ctattttattttttctgcag------------------------------
|||||||||||| |||||||||||||| || ||||| || | |   ||||| ||||||||||| ||| |||| || || ||||||||||  ||||| |||||      ||  ||  |  | | || ||||   || | | || |   |  | |   | ||| | |  | |      |  ||   || || ||||| ||                               
GGATCAGGCTGCTTTTGTTCTTAGTGTTCCGAGAAGAAAACCTGTAGATGAAACACAGGAGACACTTCGAACTTCAGCATTTCCTAGTACACATGTTAAGgtggtttttttttttttaatatattgttcccagattc-tgataaaaagaatattgtagttcctagattttgtctggttactgaattcttctttcttcaattctgaaattatttggatgattctttgcag

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|86087397|gb|DR383156.1|DR383156
EST:     AGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAG                         GAAAAATGGGGCAAGAATCTTTACATTGCATCGATTTGTTATGGTCGAACT
genomic: AGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgc ... ttttctgcagGAAAAATGGGGCAAGAATCTTTACATTGCATCGATTTGTTATGGTCGAACT
EST: gi|116431236|gb|EG473828.1|EG473828
EST:     AGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAG                         GAAAAATGGGGCAAGAATCTTTACATTGCATCGATTTGTTATGGTCGAACT
genomic: AGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgc ... ttttctgcagGAAAAATGGGGCAAGAATCTTTACATTGCATCGATTTGTTATGGTCGAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCAGGCTGCCTTTGTTCTTAGTGTGCCAAGAAGGAAGCTTACCGATGAGACACAGGAGACTCTTAGAACCTCTGCTTTTCCTAGTAATCATGTCAAGgtttgcttgctggtctcttattcctttatccattattatttggctttccaacttcttggggtgtaatatatctattttattttttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA