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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattatctaactcgcttttcacctcttgctctacattgatctctagaacatggcattgtagtagtctctgttagttttcttcagaatcgcatcgct...

Basic information

species Arabidopsis thaliana
transcript AT5G59140.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 5'ss of exon 2
TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattatctaactcgcttttcacctcttgctctacattgatctctagaaca----tggcattgtagtagtctctgttagttttcttcagaatcgcatcgct
|||| ||  ||   || ||||  || |  ||||| || || |||||| | || || |||||||| |||||||||||||||||||| || || ||||||||||     | || | ||   ||| ||| |      ||   |   ||   | | ||    |       || |||||     |  | | |    | |||   |    
TCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTACTCCAGgtaaatctttccacct---tttccacatgacatcctcattcagtcctcacaccacccctaatcccatactagtcctaactcttatgcagttggatctagtttg-

upper sequence: AT5G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G059282_T01 (Zea mays), 5'ss of exon 2
TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattatctaact--cgcttttcacc-tcttgctctacattgatctctagaacatggcattgtagtagtct---ctgttagttttcttcagaatcgcatcgct
|||| ||  ||    | ||||  ||    ||||| || ||   |||||  || || |||||||| |||||||| ||||| ||||| || || |||||||||||||  |   ||  |  | ||||  ||  || |  ||| | ||   || |    | |     ||||  |   |   | | | |||   || ||     |      
TCTCTGAGACGCGCCAGGGCGAGGTCCGCTTCCCAGAGATCCCCACCAACATCCTCGAGAAGATCTGCCAGTATTTCTATTGGTCGCTCCATTACTCCAGgttcctatgcttactttccactttcgacaatcgtcatcttctttcccctttcaggctttcacctgtaagacaatagcccgcttgttacttttaggcagcc------

upper sequence: AT5G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv06s0004g05560.t01 (Vitis vinifera), 5'ss of exon 2
TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttcca--ttatctaac---------tcgcttttcacctcttgctctacattgatctctagaacatggcattgtagtagtctctgttagttttcttcagaatcgcatcgct
|  |||||  | || |||| | ||| |||||||| || ||||||||||| || || |||||||| |||||||| |||||||||||||||||||   | ||||||    || || ||          |  |||   |      | | |   ||| | | ||| |  | ||||      | |     ||  ||||     | |          
TTGCGGAAAGGGAACATGGAGAAGTCACTTTCCCGGAGATAAGCACCACCATTCTTGAGAAGATCTGCCAGTATTTCTACTGGTCTCTTCAATTTGCGAGgttctgatttttccaatgcaaaaatgttacttaggaaaatcggttttgtgttggttt-tagtaatttgcatgaagacaattcgcatttttttttggtggga----------

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|163970539|gb|ES185392.1|ES185392
EST:     CCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: CCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|86023419|gb|DR319172.1|DR319172
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|86023423|gb|DR319176.1|DR319176
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|152038451|gb|AV823441.2|AV823441
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|86023421|gb|DR319174.1|DR319174
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|125063761|gb|EL131626.1|EL131626
EST:     TACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAG
genomic: TACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAG
EST: gi|86023424|gb|DR319177.1|DR319177
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|125115117|gb|EL165243.1|EL165243
EST:     ATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|86023422|gb|DR319175.1|DR319175
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|164127750|gb|ES163212.1|ES163212
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTT-CATATTGAGCCTGAACTGACTCTA
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTA
EST: gi|86077081|gb|DR372838.1|DR372838
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
EST: gi|164162075|gb|ES180155.1|ES180155
EST:     CCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTAGAACTGACTCTAGAGCTGA
genomic: CCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCT-GAACTGACTCTAGAGCTGA
EST: gi|125022306|gb|EL094575.1|EL094575
EST:     AGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACT
genomic: AGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACT
EST: gi|164092157|gb|ES100998.1|ES100998
EST:     GTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTAGACTCTAGAGCTGA
genomic: GTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACT-GACTCTAGAGCTGA
EST: gi|86023418|gb|DR319171.1|DR319171
EST:     ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAG                         AGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT
genomic: ATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattat ... cttttgacagAGGCAAAGAGACAGAGTTTCATATTGAGCCTGAACTGACTCTAGAGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCGGAATCGAAAGATGGCGTAGTGACTTTCCCTGATATAAGCACCACAATACTAGAGAAGATTTGCCAGTACTTCTACTGGTCTCTTCAATACTCCAGgttccattatctaactcgcttttcacctcttgctctacattgatctctagaacatggcattgtagtagtctctgttagttttcttcagaatcgcatcgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctaactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgctct