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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtggagattcatcggcagatgtatccagatttccattgactgatacagcaagacttctcgcttatatttggatttatatccctttagttgtcttacagttctttctgtgtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G53580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53580.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G35780.1 (Glycine max), 3'ss of exon 6
gttagtggagattcatcggcagatgtatccagatttccattgactgatacagcaagacttctcgcttatatttggatttatatccctttagttgtcttacagttctttctgtgtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG
                |        |  |   | |  | |  |    |  ||  |  | ||   || ||||  |   | ||| | | ||| ||||   |   ||  || | |  ||  ||||| |||||  | || |||||    ||||| |||||||||||||| |||||||| |||||||
----------------ccttgagcatgactcaaatggcctaaatgtgtgtagtcat-catcatactaatata-gttgtcatacctcattaattgt---atgatttcttattta-atgtgcagAGTTTGTGCAAGTATTATCTAACTCTCACTTGAAAATGCGTGTTTGGGAGCGGGGAGCAG
















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|125200152|gb|EL215106.1|EL215106
EST:     GAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: GAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
EST: gi|86082085|gb|DR377844.1|DR377844
EST:     TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
EST: gi|86080834|gb|DR376591.1|DR376591
EST:     TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
EST: gi|86033409|gb|DR329162.1|DR329162
EST:     TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
EST: gi|125326278|gb|EL340358.1|EL340358
EST:     GGTCCAAAGTTCGAGCATCATGAAATGTTCCCAAGCNCGAACTAACACAG                         AATTTGTTGAGGT
genomic: GGTCCAAAGTTCGAGCATCATGAAATGTTCCCA-GCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGT
EST: gi|86078439|gb|DR374196.1|DR374196
EST:     TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
EST: gi|116478499|gb|EG521091.1|EG521091
EST:     TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
EST: gi|116478497|gb|EG521089.1|EG521089
EST:     TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAG                         AATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC
genomic: TGGTCCAAAGTTCGAGCATCATGAAATGTTCCCAGCTCGAACTAACACAGgttagtggag ... gtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttggatttatatccctttagttgtcttacagttctttctgtgtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG
                          gtcttac  putative branch site (score: 3)
        atttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtggagattcatcggcagatgtatccagatttccattgactgatacagcaagacttctcgcttatatttggatttatatccctttagttgtcttacagttctttctgtgtatccgcagAATTTGTTGAGGTCTTATCACGTTCTCATTTGAAAATGCGTGTGTGGGAGCGCGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG