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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttaccttccagctttaatgtctgcctctaataaaactccaactgtggggcttgttcttgtttcagatatctaaaatgaaatctttggtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTGTAAATGCAGCTTTCTTAGCGACTCTATACAGTGATTATCTGGATGCTGC

Basic information

species Arabidopsis thaliana
transcript AT5G49720.1
intron # 4
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|47830557|gb|CK120241.1|CK120241
EST:     AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTG
genomic: AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTG
EST: gi|116458640|gb|EG501232.1|EG501232
EST:     AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTG
genomic: AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTG
EST: gi|124747683|gb|EH837813.1|EH837813
EST:     AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAGAGTTGAATCA
genomic: AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAGAGTTGAATCA
EST: gi|47829810|gb|CK119494.1|CK119494
EST:     AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTG
genomic: AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTG
EST: gi|164168560|gb|ES038939.1|ES038939
EST:     AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGC
genomic: AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGC
EST: gi|125215649|gb|EL229733.1|EL229733
EST:     TCATGTTGTCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAG
genomic: TCATG-TG-CTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAG
EST: gi|125273867|gb|EL287952.1|EL287952
EST:     AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATG                         GAGGTTTAATAGAGTTGAATCA
genomic: AGTCATGTGCTCATACTTGCCTATTTTCAACAAATTTAACAGAACCAATGgttagttacc ... gtatgtgcagGAGGTTTAATAGAGTTGAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtggggcttgttcttgtttcagatatctaaaatgaaatctttggtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTGTAAATGCAGCTTTCTTAGCGACTCTATACAGTGATTATCTGGATGCTGC
                          atctaaa  putative branch site (score: 3)
                        atatctaaaatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttaccttccagctttaatgtctgcctctaataaaactccaactgtggggcttgttcttgtttcagatatctaaaatgaaatctttggtatgtgcagGAGGTTTAATAGAGTTGAATCATGGAGCTCCACAGCCGCTGCAATATTCTGTAAATGCAGCTTTCTTAGCGACTCTATACAGTGATTATCTGGATGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC