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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttatgtagacaactaataaagatttagagctatgaattatgtatggattttacaaaaacatatttctaatcatggtttatgtgtatatatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGACAATTAGGACCCACTAATCCTCCCATCGACATTCATCCC

Basic information

species Arabidopsis thaliana
transcript AT5G44190.1
intron # 3
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|124888902|gb|EH967804.1|EH967804
EST:     CTTGGCCAGGTCATCCACCGTACTGGCATCAGCAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCATTCAAGCA
genomic: CTTGGCCAGGTCATCCACCGTACTGGCATCAGCAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCA
EST: gi|125131557|gb|EL174119.1|EL174119
EST:     CAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGA
genomic: CAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGA
EST: gi|125224642|gb|EL238727.1|EL238727
EST:     TACTGGCATCAGCAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGT
genomic: TACTGGCATCAGCAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGT
EST: gi|125276669|gb|EL290754.1|EL290754
EST:     TCCACCGTACTGGCATCAGCAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAG
genomic: TCCACCGTACTGGCATCAGCAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAG
EST: gi|124733745|gb|EH825147.1|EH825147
EST:     CAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGA
genomic: CAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGA
EST: gi|125258308|gb|EL272393.1|EL272393
EST:     CTTGGCCAGGTCATCCACCGTACTGGCATCAGCAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCA
genomic: CTTGGCCAGGTCATCCACCGTACTGGCATCAGCAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCA
EST: gi|125296724|gb|EL310809.1|EL310809
EST:     CTTGGCCAGGTCATCCACCGTACTGGCATCAGCAACCACTCTATCCACAG                         GGATATGGTATGGCATCATCGAATCA
genomic: CTTGGCCAGGTCATCCACCGTACTGGCATCAGCAACCACTCTATCCACAGgtaataataa ... atatgtgtagGGATATGGTATGGCATCATCGAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggattttacaaaaacatatttctaatcatggtttatgtgtatatatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGACAATTAGGACCCACTAATCCTCCCATCGACATTCATCCC
                      ttctaat  putative branch site (score: 2)
     attttacaaaaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttatgtagacaactaataaagatttagagctatgaattatgtatggattttacaaaaacatatttctaatcatggtttatgtgtatatatgtgtagGGATATGGTATGGCATCATCGAATCATTCAAGCATCGGTGTTCCCACAAGACAATTAGGACCCACTAATCCTCCCATCGACATTCATCCC

- - - - - - -caactaa
- - - - - - - - - - - - gatttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttat