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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTACAACTGTGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgttcctcctcggaagaatgaatcatctgttcttcttatagctataatggtgtaattatgtcctctgtttgattttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G28190.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28190.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G106928_T02 (Zea mays), 5'ss of exon 2
GTCCTACAACTGTGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgttcctcctcggaagaatgaatcatctgttcttcttatagctataatggtgtaattatgtcctctgtttgattttgcag
| ||||||||||||||||| ||||||||||| || || || || | |||||| || || ||||| || ||  |  || ||   ||  |    |||    |  | | || || |  ||| ||  || |      |  ||| |||||||||
GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATGGCTTCCACCTCgtgagttttgttatcttcaatagctttgggcattaacttct-tcattgcaaacatgatg--atgaca----caatttcattttgcag

upper sequence: AT2G28190.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G30260.1 (Glycine max), 5'ss of exon 2
GTCCTACAACTGTGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgttcctcctcggaagaatgaatcatctgttcttcttatagctataatggtgtaattatgtcctctgtttgattttgcag
| || |||||||| | ||||||| |  ||||||| ||||| ||||||||||| ||||||||||| || ||      |          | |  |   | |     | ||      | | |||  ||| | |  ||| |||    ||||||
GCCCAACAACTGTTACTGTTCGTGTTTCTGGTCTTACTCCTGGGCCTCATGGTTTTCATCTCgtgagttttgaggcctctttctatgtcatcccgttttcgaaatcattttctaacttgtgctatttt-tgttctcttt---cttgcag
















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|124770104|gb|EH860234.1|EH860234
EST:     CCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCGACAG
genomic: CCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|125130937|gb|EL173857.1|EL173857
EST:     GTTCGGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAA
genomic: GTTC-GTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAA
EST: gi|125033156|gb|EL105425.1|EL105425
EST:     CCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: CCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|125269195|gb|EL283280.1|EL283280
EST:     TGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|301502082|gb|HO207622.1|HO207622
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|116429789|gb|EG472381.1|EG472381
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|163993357|gb|ES074766.1|ES074766
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCT
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCT
EST: gi|125258299|gb|EL272384.1|EL272384
EST:     TCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|125315095|gb|EL329180.1|EL329180
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGG
EST: gi|124951299|gb|EL026682.1|EL026682
EST:     TTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGGACCACATT
genomic: TTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGGACCACATT
EST: gi|164146287|gb|ES034714.1|ES034714
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGG
EST: gi|125257117|gb|EL271202.1|EL271202
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCT
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCT
EST: gi|125187016|gb|EL201970.1|EL201970
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGG
EST: gi|124888922|gb|EH967824.1|EH967824
EST:     TGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|125054045|gb|EL124919.1|EL124919
EST:     GAATGCTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGGA
genomic: GAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGGA
EST: gi|116462064|gb|EG504656.1|EG504656
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|86080763|gb|DR376520.1|DR376520
EST:     ATGTTCGTATCACTGGTCTCACTCCAGGSCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: ATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|125260896|gb|EL274981.1|EL274981
EST:     CGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: CGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|125192286|gb|EL207240.1|EL207240
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAGG
EST: gi|124716462|gb|EH807864.1|EH807864
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTA
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTA
EST: gi|125258665|gb|EL272750.1|EL272750
EST:     CCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: CCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
EST: gi|116438236|gb|EG480828.1|EG480828
EST:     TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTC                         CATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG
genomic: TGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgt ... gattttgcagCATGAGTTTGGTGATACAACTAATGGATGTATCTCAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTACAACTGTGAATGTTCGTATCACTGGTCTCACTCCAGGGCCTCATGGATTTCATCTCgtaagcttgttcctcctcggaagaatgaatcatctgttcttcttatagctataatggtgtaattatgtcctctgtttgattttgcag

- - - - - - - - - - - - - - - - - - - - - - -  CATGGA