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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactcttgcttctttcttatctcaaaccattaaaacatgaattggttcttatgagtgaaaacattttctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTAGAATGATGGCTGCTAATCTCTACTTCTCCCAGATAGAAGATCTTATGTT

Basic information

species Arabidopsis thaliana
transcript AT2G42600.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 6
gtacactcttgcttctttcttat-ctcaaaccattaaaacatgaattggttcttatgagtgaaaacattttctgaa-tctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTAGAATGATGGCTGCTAATCTCTACTTCTCCCAGATAGAAGATCTTATGTT
|||   |    ||    | | ||  |   | |||    |  | | |  |   |||||  |  ||   |  | || | |  |||||| ||  |||| || || || |||||||| || |||||| | |||||||||||||||||||||||  | ||||   | |||||||| ||||| |||||
gtatgttacatctatcatatcatgtttgcaacatagttaattaattgtgaaattatggttttaatattgatgtggactacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGACGTATGCCTGTTAGCTAGAATGATGGCTGCTAACTTATACTATGCACAGATAGAGGATCTGATGTT

upper sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
---------gtacactcttgcttctttc----ttat-ctcaaaccattaaaacatg-aattg--gttcttatga-----gtgaaaacatt-ttctgaatc-----------tagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTAGAATGATGGCTGCTAATCTCTACTTCTCCCAGATAGAAGATCTTATGTT
          | | ||||  ||| |||      |||  |  |     | || |||| || ||  ||||  | ||     ||| ||| ||   ||||||              ||| || ||  |||| || || || |||||||| ||||||||||| || ||||||||||||||||||||| | ||     ||||||||||||| || |||||
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
















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|47828387|gb|CK118071.1|CK118071
EST:     CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATG                         GAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTA
genomic: CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATGgtacactctt ... ctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTA
EST: gi|124760307|gb|EH850437.1|EH850437
EST:     CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATG                         GAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATG
genomic: CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATGgtacactctt ... ctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATG
EST: gi|125194870|gb|EL209824.1|EL209824
EST:     TCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATG                         GAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCT
genomic: TCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATGgtacactctt ... ctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCT
EST: gi|125045658|gb|EL117927.1|EL117927
EST:     CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATG                         GAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTAT
genomic: CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATGgtacactctt ... ctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTAT
EST: gi|116416335|gb|EG458927.1|EG458927
EST:     CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATG                         GAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTA
genomic: CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATGgtacactctt ... ctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTA
EST: gi|124750400|gb|EH840530.1|EH840530
EST:     CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATG                         GAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTT
genomic: CAATGCGCCTCTCATTCAGTTCTCTTCTTGGATGGGCGGAGACCGTGATGgtacactctt ... ctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaccattaaaacatgaattggttcttatgagtgaaaacattttctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTAGAATGATGGCTGCTAATCTCTACTTCTCCCAGATAGAAGATCTTATGTT
                                       cattttct  CT-rich tract
      attaaaacatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacactcttgcttctttcttatctcaaaccattaaaacatgaattggttcttatgagtgaaaacattttctgaatctagGAAACCCGCGAGTAACTCCTGAAGTTACAAGAGATGTATGCTTATTAGCTAGAATGATGGCTGCTAATCTCTACTTCTCCCAGATAGAAGATCTTATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT