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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttttttctttctttctccttataacatctatctctctttattacattcagagttgttgagctcatgagtttgctttgttttttttactgatgtgtttatagGGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGATGAGTATCACTTCAAGCACGTGGAGCTTTGATCTATCTAATAGTCATCT

Basic information

species Arabidopsis thaliana
transcript AT2G24490.1
intron # 9
splice site 3'
intron type U2

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|19797959|gb|AU229559.1|AU229559
EST:     TGAAATTGCTCAGCAGTTGAAAATCCCAAAAAACAAGCTAGA                         G
genomic: TGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAGCTAGAgtatgctttt ... gtgtttatag-
EST: gi|19797959|gb|AU229559.1|AU229559
EST:     TGAAATTGCTCAGCAGTTGAAAATCCCAAAAAACAAGCTAGA                         G
genomic: TGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAGCTAGAgtatgctttt ... gtgtttatag-
EST: gi|116392123|gb|EG434715.1|EG434715
EST:     CATATCGATGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAACTAGA                         GGGCGTTGTTCAATCGCTGGAAGGAGATGGTCTAATATACTCGACAATCGA
genomic: CATATCGATGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAGCTAGAgtatgctttt ... gtgtttatagGGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGA
EST: gi|86075466|gb|DR371223.1|DR371223
EST:     CATATCGATGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAGCTAGA                         GGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGA
genomic: CATATCGATGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAGCTAGAgtatgctttt ... gtgtttatagGGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGA
EST: gi|116392116|gb|EG434708.1|EG434708
EST:     CATATCGATGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAACTAGA                         GGGCGTTGTTCAATCGCTGGAAGGAGATGGTCTAATATACTCGACAATCGA
genomic: CATATCGATGAAATTGCTCAGCAGTTGAAGATCCCAAAAAACAAGCTAGAgtatgctttt ... gtgtttatagGGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagagttgttgagctcatgagtttgctttgttttttttactgatgtgtttatagGGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGATGAGTATCACTTCAAGCACGTGGAGCTTTGATCTATCTAATAGTCATCT
                                      tactgat  putative branch site (score: 2)
                           tttgttttttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttttttctttctttctccttataacatctatctctctttattacattcagagttgttgagctcatgagtttgctttgttttttttactgatgtgtttatagGGGCGTTGTTCAATCACTGGAAGGAGATGGTCTAATATACTCGACAATCGATGAGTATCACTTCAAGCACGTGGAGCTTTGATCTATCTAATAGTCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT