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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatacacctgggctctttttttacttctagtagaattctgtgtatacaactcttttaatatatcttttttgtggattattttgtaacttccacttcttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG

Basic information

species Arabidopsis thaliana
transcript AT1G23190.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 11
gtattatacacctgggctctttttttacttcta-gtagaattctgtgtatacaactcttttaatatatcttt-----tttgtggattattt--tgtaacttccacttcttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG
                 |  |     |||| || | ||   ||||    ||  |  | ||||| || ||| |      |  | |  || ||     ||  |    || |   |  |||||||||||||| |||||||| |||||||| |||||||| |  |||||| | ||||||||||||
----------------ttgatcccccacttgtatgcagctatctgacctta-gatgcatttaaaatttctctatgcactgataggctacttacgacaatctaatgttgtaaatgcagGAGCATGCCAACATCAGCTGCCCTTGATGTTGTTGCAAAGAATTTGAATCTCAAGTTCTTTGAG

upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 11
gtattatacacctgggctctttttttacttcta-gtagaattctgtgtatacaactcttttaatatatcttttt----tgtggattattt-tgtaacttccac-ttcttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG
                 || | ||   ||| || | ||   || | || |   |  | ||| | || ||| | |    ||   | || || ||| | | |    || |  |   |||||||||||||| || ||||| |||||||| |||||||| |  |||||  | ||||||||||||
---------------tttcatcttccgcttgtatgcagctgtccg-gtcttagatgcatttgaaatttctctatgcactgaacactacttatgttattccattattgtaataacagGAGCATGCCAACATCTGCTGCCCTTGATGTTGTTGCAAAGAATTTGAACCTTAAGTTCTTTGAG
















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|164086223|gb|ES115104.1|ES115104
EST:     GGTGCCATCCCGTACTTCAGCTCTGGTTTGAAAGGTGTTGCAAG                         GAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTT
genomic: GGTGCCATCCCGTACTTCAGCTCTGGTTTGAAAGGTGTTGCAAGgtattataca ... cttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTT
EST: gi|47831641|gb|CK121325.1|CK121325
EST:     GCTATTGGTGCCATCCCGTACTTCAGCTCTGGTTTGAAAGGTGTTGCAAG                         GAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAA
genomic: GCTATTGGTGCCATCCCGTACTTCAGCTCTGGTTTGAAAGGTGTTGCAAGgtattataca ... cttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAA
EST: gi|124982142|gb|EL054969.1|EL054969
EST:     GCTATTGGTGCCATCCCGTACTTCAGCTCTGGTTTGAAAGGTGTTGCAAG                         GAGCATGCCAA
genomic: GCTATTGGTGCCATCCCGTACTTCAGCTCTGGTTTGAAAGGTGTTGCAAGgtattataca ... cttgttttagGAGCATGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttaatatatcttttttgtggattattttgtaacttccacttcttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG
                              ttgtaac  putative branch site (score: 2)
                                    cttccacttcttgttt  CT-rich tract
     taatatatcttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatacacctgggctctttttttacttctagtagaattctgtgtatacaactcttttaatatatcttttttgtggattattttgtaacttccacttcttgttttagGAGCATGCCAACCTCAGCTGCTCTTGATGTCGTTGCAAAAAGCTTGAATTTGAAGTTCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG