Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtttttttgcatccatacaagttcttagttacttgaatcgtttcctatttttttcattcgatctgtaatgtttttagggtttaataacttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG

Basic information

species Arabidopsis thaliana
transcript AT3G14290.1
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|125244374|gb|EL258459.1|EL258459
EST:     AGGAACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTG                         ACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCA
genomic: AGGAACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCA
EST: gi|164185085|gb|ES009623.1|ES009623
EST:     ACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCCG                         ACATTGAGGTTTATCTCAGATCGAAA
genomic: ACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAA
EST: gi|124882843|gb|EH961745.1|EH961745
EST:     GGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTG                         ACATTGAGGTTTATCT
genomic: GGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCT
EST: gi|152033857|gb|BP817785.2|BP817785
EST:     GGAACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAACTTCTCAGCTG                         ACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG
genomic: GGAACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAA-TTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG
EST: gi|116474984|gb|EG517576.1|EG517576
EST:     AGATCAATTCTCAGCTG                         ACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG
genomic: AGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG
EST: gi|163971728|gb|ES048604.1|ES048604
EST:     GTAGATCAATTCTCAGCTG                         ACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTC
genomic: GTAGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTC
EST: gi|163990549|gb|ES114655.1|ES114655
EST:     GGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTG                         ACATTGAGGTTTATCTCAGATCGAAATCG
genomic: GGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCG
EST: gi|86075577|gb|DR371334.1|DR371334
EST:     AGGAACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTG                         ACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG
genomic: AGGAACTGGGAAGAGTTTGTTTCTTCGATTCGTAGATCAATTCTCAGCTGgtaaagtttt ... ttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatttttttcattcgatctgtaatgtttttagggtttaataacttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG
                                      taataac  putative branch site (score: 1)
                                            cttttgt  CT-rich tract
                                    tttaataacttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtttttttgcatccatacaagttcttagttacttgaatcgtttcctatttttttcattcgatctgtaatgtttttagggtttaataacttttgtgcagACATTGAGGTTTATCTCAGATCGAAATCGAGAAGAAGATGTTTCTCACTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG