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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatctacgccattcttgccaatgttgatacctttcagtttattttagtacttgaatctcaacttctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT2G34560.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 5
--------------gtatgttatctacgc----cattcttgccaatgttgatacctttcagttt--attttagtacttgaatctcaacttctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAG
               | |  |||  || |    |    |  |||| | | || | ||  | | |  |||| |  |   |     | |   ||      |||||||||| |||||| ||| | ||||||||||| ||||| |||||||||||||| || || ||||||
ttcatttttggaagatttactatgaacacatgacgaattgcccaaagataatgctttgaaatcttcatttcacaataagctgacctatcccttcatctagGTACTTTACTGGTCTTCTATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAG
















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|124720187|gb|EH811589.1|EH811589
EST:     GCTAAAAAGTTGCTCAAAGAAGCTGTGGTGATGCCTATAAAATACCCCAC                         GTACTTTAATGGTCTACTAACCCCATGGAAAGGAATTCTTCTTTTTGGTCC
genomic: GCTAAAAAGTTGCTCAAAGAAGCTGTGGTGATGCCTATAAAATACCCCACgtatgttatc ... ctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCC
EST: gi|124771328|gb|EH861458.1|EH861458
EST:     TGCCTATAAAATACCCCAC                         GTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCC
genomic: TGCCTATAAAATACCCCACgtatgttatc ... ctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCC
EST: gi|163991033|gb|ES146261.1|ES146261
EST:     AAAGAAGCTGTGGTGATGCCTATAAAATA-CCCAC                         GTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCC
genomic: AAAGAAGCTGTGGTGATGCCTATAAAATACCCCACgtatgttatc ... ctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCC
EST: gi|164051343|gb|ES162556.1|ES162556
EST:     GCTAAAAAGTTGCTCAAAGAAGCTGTGGTGATGCCTATAAAATACCCCAC                         GTACTTTAATGGTCTACTAACTCCATGGAAAGG
genomic: GCTAAAAAGTTGCTCAAAGAAGCTGTGGTGATGCCTATAAAATACCCCACgtatgttatc ... ctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttgatacctttcagtttattttagtacttgaatctcaacttctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAG
                                           ttctgat  putative branch site (score: 3)
                                          cttct  CT-rich tract
            tttcagtttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttatctacgccattcttgccaatgttgatacctttcagtttattttagtacttgaatctcaacttctgatgtcagGTACTTTAATGGTCTACTAACTCCATGGAAAGGAATTCTTCTTTTTGGTCCTCCTGGTACCGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA