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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccctagattcaaccacactttatgttttactccttctacacactttaatttctggtatcaagttgatggtatctaacattgcgttcatgaatcttctcaatagGTTACCGGCGATTGGAATGTTACCCGGTAGGGGTGGACCAACCTGTCGTGTTGGGATATAAACAG

Basic information

species Arabidopsis thaliana
transcript AT3G51950.1
intron # 8
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|164182986|gb|EL988558.1|EL988558
EST:     CTACACTCTCCGACTCCTTCAACTCTTTCAACTACCAAATGCCAAG                         GTTACCGGCGATTGGAATGTTACCCGGTAGGGGTGGACCAACCT
genomic: CTACACTCTCCGACTCCTTCAACTCTTTCAACTACCAAATGCCAAGgtccctagat ... ttctcaatagGTTACCGGCGATTGGAATGTTACCCGGTAGGGGTGGACCAACCT
EST: gi|164221905|gb|ES063501.1|ES063501
EST:     CCTTCTACACTCTCCGACTCCTTCAACTCTTTCAACTACCAAATGCCAAG                         GTTACCGGCGATTGG
genomic: CCTTCTACACTCTCCGACTCCTTCAACTCTTTCAACTACCAAATGCCAAGgtccctagat ... ttctcaatagGTTACCGGCGATTGG
EST: gi|164185274|gb|ES129974.1|ES129974
EST:     CCTTCTACACTCTCCGACTCCTTCAACTCTT-CAACTACCAAATGCCAAG                         GTTACCGGCGATTGG
genomic: CCTTCTACACTCTCCGACTCCTTCAACTCTTTCAACTACCAAATGCCAAGgtccctagat ... ttctcaatagGTTACCGGCGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctggtatcaagttgatggtatctaacattgcgttcatgaatcttctcaatagGTTACCGGCGATTGGAATGTTACCCGGTAGGGGTGGACCAACCTGTCGTGTTGGGATATAAACAG
                      atctaac  putative branch site (score: 2)
                                           tcttctc  putative PPT
                     tatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccctagattcaaccacactttatgttttactccttctacacactttaatttctggtatcaagttgatggtatctaacattgcgttcatgaatcttctcaatagGTTACCGGCGATTGGAATGTTACCCGGTAGGGGTGGACCAACCTGTCGTGTTGGGATATAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA