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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcctctattcactttagtatatagtctatgagtcgtttttaaagtaacacaatttattacatttttggtgaaattctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTGAACTTTTATCAAACAGTGAATCCTGATGTTGCAAAGATGTTTCACCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G60640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 2
-------------gtatgtttcctctattcactttagtatat-agtctatgagtcgtttttaaagtaacacaatttattacatttttggtgaa-attctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTGAACTTTTATCAAACAGTGAATCCTGATGTTGCAAAGATGTTTCACCTTG
              ||  ||       |   || || ||  | | | |||||     || |    |   |   ||||||    || || || | | | | ||||||  ||||   ||  |||||  ||||||||| |    ||| || ||||| || ||||||||||| |||||||||||||| |||||| | || ||  |||
ttgaatctctggattaaattataggcttgagctgtaatacttgaatgtatgaaa---ttgttggtttttatgctttatttatcttgtgatgcataatgtgcagGGTCCTGAGAGTGAGGAGCTTGCTGCTGCTTCAAGGCTTGAGGATGATGTCAATTTTTATCAAACTGTGAATCCTGATGTGGCAAAGCTTTTCCATATTG
















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|86064529|gb|DR360286.1|DR360286
EST:     TTGTTTTGGGATACTTGAACTCCTTGGTG                         GGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTG
genomic: TTGTTTTGGGATACTTGAACTCCTTGGTGgtatgtttcc ... aattctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTG
EST: gi|86064531|gb|DR360288.1|DR360288
EST:     TTGTTTTGGGATACTTGAACTCCTTGGTG                         GGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTG
genomic: TTGTTTTGGGATACTTGAACTCCTTGGTGgtatgtttcc ... aattctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTG
EST: gi|86054030|gb|DR349787.1|DR349787
EST:     TGTTGACTTCTGGGAACAAAGTTGTTTTGGGATACTTGAACTCCTTGGTG                         GGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTG
genomic: TGTTGACTTCTGGGAACAAAGTTGTTTTGGGATACTTGAACTCCTTGGTGgtatgtttcc ... aattctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgagtcgtttttaaagtaacacaatttattacatttttggtgaaattctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTGAACTTTTATCAAACAGTGAATCCTGATGTTGCAAAGATGTTTCACCTTG
               aagtaac  putative branch site (score: 2)
         tttttaaagtaacaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcctctattcactttagtatatagtctatgagtcgtttttaaagtaacacaatttattacatttttggtgaaattctacagGGTGTTGAGCACGATCAGCTTAATGCTGCTTCCAAAGCTGAAGACGATGTGAACTTTTATCAAACAGTGAATCCTGATGTTGCAAAGATGTTTCACCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG