Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaatcattcatcattcatgttttaagagtaaatgtatgaatcttgttgagatagtgtttttttttagttaagtatcaataaattgttgtatgtggaagatttttatgtataggcattgcttttaacaagaacgaatgaaactacttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCTCGGGTTTGGTGCTTCGGATAAGCCACCTGGTTTTAGCTATACCATGGAG

Basic information

species Arabidopsis thaliana
transcript AT5G38520.1
intron # 1
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|86032551|gb|DR328304.1|DR328304
EST:     ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
genomic: ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
EST: gi|124781999|gb|EH871942.1|EH871942
EST:     CTGTTCTTTTGGTTCATGGCTTTGGTGCTTTCTATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
genomic: CTGTTCTTTTGGTTCATGGCTTTGGTGC-TTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
EST: gi|86032546|gb|DR328299.1|DR328299
EST:     ACTGTTCTTTTGGTTCATGGCTTTGGTGCTYCTANTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAAC
genomic: ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAAC
EST: gi|86032548|gb|DR328301.1|DR328301
EST:     ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTC
genomic: ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTC
EST: gi|86073182|gb|DR368939.1|DR368939
EST:     ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
genomic: ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
EST: gi|86032545|gb|DR328298.1|DR328298
EST:     ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
genomic: ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
EST: gi|86032549|gb|DR328302.1|DR328302
EST:     ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
genomic: ACTGTTCTTTTGGTTCATGGCTTTGGTGCTTCTATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
EST: gi|125315101|gb|EL329186.1|EL329186
EST:     ATTCCTCACTGGCGAAG                         GAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT
genomic: ATTCCTCACTGGCGAAGgtattaatca ... acttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttatgtataggcattgcttttaacaagaacgaatgaaactacttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCTCGGGTTTGGTGCTTCGGATAAGCCACCTGGTTTTAGCTATACCATGGAG
                      ttttaac  putative branch site (score: 2)
                                           ctactttt  putative PPT
     ttatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaatcattcatcattcatgttttaagagtaaatgtatgaatcttgttgagatagtgtttttttttagttaagtatcaataaattgttgtatgtggaagatttttatgtataggcattgcttttaacaagaacgaatgaaactacttttgcagGAACATAAATGCTTTGTCTAAAAACCATACAGTGTATGCAATTGATCTTCTCGGGTTTGGTGCTTCGGATAAGCCACCTGGTTTTAGCTATACCATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA