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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttaatctaatcccaatatctaccttgacttaaaaaaaggaacctacaatcattctcaattcctgaattttccatttgatctttatgtagGAGATGGTGGACTTTCTTGTCGATATTTGGTACGATGAAGGCCTTTACGATTAGAAGAATCTAACAATGCCACGAACTAGATTGACAAAGAACAAAGGAG

Basic information

species Arabidopsis thaliana
transcript AT3G54880.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S29_334V6.1 (Physcomitrella patens), 3'ss of exon 6
------gtaagctttaatctaatcccaatatctaccttgacttaaaaaaaggaacctacaatcattctcaattcctgaattttccatttgatctttat--gtagGAGATGGTGGACTTTCTTGTCGATATTTGGTACGATGAAGGCCTTTACGATTAGA----AGAATCTAACAATGCC-ACGAACTAGATTGACAAAGAACAAAGGAG
      |  |    ||   | || | ||  ||| |    |  |  |   |   |  ||   |  |     |||| | || |       ||  ||  ||  ||||||||||||||| |||||||||||| | ||| |  | |||||||| ||||| ||||    |||  ||    |||   |     || |  |    || || |     
tgttgcgagaatagtatggtgatgctaa--tctgctgcaatgttgatggatttatttatttttgtat--gattcatcaactccagtactggactaaatttgtagGAGATGGTGGATTTTCTTGTCGATGTATGGGAGCAAGAAGGCCTCTACGAGTAGACTACAGATGCTGGTGATGAAGATTTCTTATACGGTTTCAGTACTA-----
















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|164079234|gb|ES181514.1|ES181514
EST:     CCTTTCTCTGAGTCGATTCCTTTACCC                         GAGATGGTGGACTTTCTTGTCGATATTTGGTACGATGAAGGCCTTTACGAT
genomic: CCTTTCTCTGAGTCGATTCCTTTACCCgtaagcttta ... ctttatgtagGAGATGGTGGACTTTCTTGTCGATATTTGGTACGATGAAGGCCTTTACGAT
EST: gi|125148463|gb|EL182120.1|EL182120
EST:     AAGATCTTCTCTCAACTCATGAACCTTTCTCTGAGTCGATTCCTTTACCC                         GAGATGGTGGACTTTCTTGT
genomic: AAGATCTTCTCTCAACTCATGAACCTTTCTCTGAGTCGATTCCTTTACCCgtaagcttta ... ctttatgtagGAGATGGTGGACTTTCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggaacctacaatcattctcaattcctgaattttccatttgatctttatgtagGAGATGGTGGACTTTCTTGTCGATATTTGGTACGATGAAGGCCTTTACGATTAGAAGAATCTAACAATGCCACGAACTAGATTGACAAAGAACAAAGGAG
                                      atttgat  putative branch site (score: 5)
                                            tctttat  CT-rich tract
                            tgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttaatctaatcccaatatctaccttgacttaaaaaaaggaacctacaatcattctcaattcctgaattttccatttgatctttatgtagGAGATGGTGGACTTTCTTGTCGATATTTGGTACGATGAAGGCCTTTACGATTAGAAGAATCTAACAATGCCACGAACTAGATTGACAAAGAACAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG