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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacacacacacacacactagattaatgtaaagttgaaagtagaaatcttgagaaagtctattgagcggcattaagagtagagttcttacacgagatttgacttgtagGGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTTGGTGTCCTCGAGAGCACTAAGAGAACACTTGCACAGAGACGTCCCAATA

Basic information

species Arabidopsis thaliana
transcript AT4G39460.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os07g19460.1 (Oryza sativa), 3'ss of exon 11
------------------------------------------------------------------gtagacacacacacacacactagat-taatgtaaagttgaaagtagaaatcttgagaaagtctattgagcggcattaagagtagagttcttacacgagatttgactt-----gtagGGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTTGGTGTCCTCGAGAGCACTAAGAGAACACTTGCACAGAGACGTCCCAATA
                                                                   |      | ||     |    ||| |  |       ||| |    |||| |||    |    | |||     | |     | | || | |   |  ||| | |||      | ||||||||| |||||| || || ||||| || ||||| ||||| ||||||||||||||  | ||||  || |||  ||  || ||  ||||      |  ||
gtaaattatccttgtcaaatagaaaattttatcattttaggtaggacaggcagacgctaaaatatcatgtctgaatactttaccttgggatatgtttctggcctgataaagcaaatattggagtaacaaactgaagcttagttctgttggtgtgcatttgcttgatattactctgctggcagGGTATTGAGCCAAGGGTATTATGGATTGGCATTGGTGGATCCATCTTCTTTGGTGTTTTGGAGAAAACGAAGTCAATTCTAGCTGAGAGGAACAGCCGTA
















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|86082868|gb|DR378627.1|DR378627
EST:     ACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG                         GGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTT
genomic: ACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAGgtagacacac ... tgacttgtagGGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTT
EST: gi|125085138|gb|EL145089.1|EL145089
EST:     ACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG                         GGTATTGGGCCAAGAGTGTTGTGG
genomic: ACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAGgtagacacac ... tgacttgtagGGTATTGGGCCAAGAGTGTTGTGG
EST: gi|124721060|gb|EH812462.1|EH812462
EST:     CTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTACTTAAAG                         GGTATTGGGCCAAGAGTGTTGTGGATA
genomic: CTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCT-CTTAAAGgtagacacac ... tgacttgtagGGTATTGGGCCAAGAGTGTTGTGGATA
EST: gi|125313720|gb|EL327805.1|EL327805
EST:     ACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAG                         GGTATTGGGCCAAGAGTG
genomic: ACTGTGTTCAAACAATTGTAAGAGAGGAAGGAGCTCCTGCTCTCTTAAAGgtagacacac ... tgacttgtagGGTATTGGGCCAAGAGTG
EST: gi|124957192|gb|EL032052.1|EL032052
EST:     AGAGGAAGGAGCTCCTGCTCTCTTAAAG                         GGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTT
genomic: AGAGGAAGGAGCTCCTGCTCTCTTAAAGgtagacacac ... tgacttgtagGGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtctattgagcggcattaagagtagagttcttacacgagatttgacttgtagGGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTTGGTGTCCTCGAGAGCACTAAGAGAACACTTGCACAGAGACGTCCCAATA
                 attaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacacacacacacacactagattaatgtaaagttgaaagtagaaatcttgagaaagtctattgagcggcattaagagtagagttcttacacgagatttgacttgtagGGTATTGGGCCAAGAGTGTTGTGGATAGGTATTGGAGGATCAATCTTCTTTGGTGTCCTCGAGAGCACTAAGAGAACACTTGCACAGAGACGTCCCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA