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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagctacacatttttaacctttgggatgatacgatctgctatggtttgctcttttggttatttctgattagattggactttgtggatatgttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTG

Basic information

species Arabidopsis thaliana
transcript AT2G20360.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g57180.2 (Oryza sativa), 3'ss of exon 4
tgagctacacatttttaacctttgggatgatacgatctg---ctatggtttgctcttttggttatttc-tgattagat-tggactttgtggatatgttgttt-cagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTG
    |||  ||||| |||| ||     || | |    ||    |||  ||  |        || |||  ||  | | | |  ||| |||  ||    | |   ||| |  | ||||| || || || || ||||||| ||| || ||||||| ||||||||| || |  || |||||||| |||||||||||||| || |||||||
----ctat-catttgtaactttctttttgctgcatcatgacaatataattcccatcaagacttcttttgtggctggctattaactgtgtt-atggactatgcacagATTTCAAAGGAGCATGGGGGTATCATGAGATTTATCCAGGTTTCTTCCCTAGGAGCATCGGCCTCTTCTCCTTCTAGAATGCTGAGGGCCAAGGCTGCTG
















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|116387772|gb|EG430364.1|EG430364
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116483643|gb|EG526235.1|EG526235
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377195|gb|EG419787.1|EG419787
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|164073255|gb|EL975586.1|EL975586
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTG
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTG
EST: gi|116377193|gb|EG419785.1|EG419785
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|125271808|gb|EL285893.1|EL285893
EST:     TGAGAAACTTGCATTG                         GTGGCCAAGGAACTACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCT
genomic: TGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAAC-ACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCT
EST: gi|86048714|gb|DR344469.1|DR344469
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|86048691|gb|DR344446.1|DR344446
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377192|gb|EG419784.1|EG419784
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377191|gb|EG419783.1|EG419783
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377190|gb|EG419782.1|EG419782
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377199|gb|EG419791.1|EG419791
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116387790|gb|EG430382.1|EG430382
EST:     TTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: TTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377200|gb|EG419792.1|EG419792
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|47828656|gb|CK118340.1|CK118340
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377196|gb|EG419788.1|EG419788
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|116377187|gb|EG419779.1|EG419779
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
EST: gi|124997238|gb|EL069507.1|EL069507
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATA
EST: gi|86048696|gb|DR344451.1|DR344451
EST:     ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTG                         GTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA
genomic: ATTTCAGTTTTGAAGATGCGAATCATCATATTGCTGAGAAACTTGCATTGgtatgtgttt ... gttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctcttttggttatttctgattagattggactttgtggatatgttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTG
                 ttctgat  putative branch site (score: 3)
                                              ttgtttc  putative PPT
             ttatttct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagctacacatttttaacctttgggatgatacgatctgctatggtttgctcttttggttatttctgattagattggactttgtggatatgttgtttcagGTGGCCAAGGAACACGGTGGGATAATGAGATATATTCAAGTTTCTTGCCTAGGAGCTTCTGTGTCATCTCCTTCAAGAATGCTGAGGGCAAAAGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - ctacaca
- - - - - - - - - - - - - - - - - - ctgctat