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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattttgtgttgcattgaaaaactactttggatgaatataactatgcaatttctgttgagtttcattgatgaagtttgtgtaaatcatactatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCTGCAGAGTATGCGGGTGTGAAGATCGAGGAGTCCGCAGACTTTCAGATGG

Basic information

species Arabidopsis thaliana
transcript AT1G57720.1
intron # 2
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|124794028|gb|EH883707.1|EH883707
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATA
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATA
EST: gi|152035102|gb|BP844635.2|BP844635
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
EST: gi|116434996|gb|EG477588.1|EG477588
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
EST: gi|116473109|gb|EG515701.1|EG515701
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
EST: gi|125049812|gb|EL122081.1|EL122081
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATT
EST: gi|116434993|gb|EG477585.1|EG477585
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
EST: gi|152035939|gb|BP865394.2|BP865394
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
EST: gi|116410809|gb|EG453401.1|EG453401
EST:     TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTG                         GTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT
genomic: TCAGAAAATCTCCGAGTTCGTATATCTTCTCCGTTTGAGCAATGGCGTTGgtaagtactc ... tatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatttctgttgagtttcattgatgaagtttgtgtaaatcatactatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCTGCAGAGTATGCGGGTGTGAAGATCGAGGAGTCCGCAGACTTTCAGATGG
                  cattgat  putative branch site (score: 4)
                                   taaatcatactattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattttgtgttgcattgaaaaactactttggatgaatataactatgcaatttctgttgagtttcattgatgaagtttgtgtaaatcatactatttatcagGTCATGCACACATACAAGGGAAACAAAGGTGCCAATAAGGCACTTATTGCTGCAGAGTATGCGGGTGTGAAGATCGAGGAGTCCGCAGACTTTCAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG