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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatgtagcttttaaagaaatgacatttttttcacaggtctaatggttttcatgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGGAACACAGACTATGGAGATCTGAGAAAGTATATATCTGGCTTTTTCGACA

Basic information

species Arabidopsis thaliana
transcript AT5G53850.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53850.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 9
----------------------gtatgttcatgtagcttttaaagaaatg-----acatttttttcacag-----gtctaatggtt-ttcatgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGGAACACAGACTATGGAGATCTGAGAAAGTATATATCTGGCTTTTTCGACA
                      || || | || |     | || |  ||       |||| | ||  ||          | || || |||   | || |||| |||||||||||||| |||||  | || || |||| |||||| |||||  ||||| ||||||| || || ||||| ||| ||| ||| ||||||||||
gctaaacgttagatgctgttctgtttgattatttgatggtaaaggccatctttttgcattctgttggcaatgtaaactcactgattgttccctcaaacagGTGTACATATATTCTAGTGGTAGCAGGTTGGCTCAAAGGCTTCTATTTGGATACACAAACTATGGGGACCTAAGAAAATATTTATGTGGATTTTTCGACA
















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|125158298|gb|EL186959.1|EL186959
EST:     AGAAATGGCATTCTTCAGGAATTAAG                         GTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
genomic: AGAAATGGCATTCTTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
EST: gi|164100447|gb|ES211374.1|ES211374
EST:     GATGCTTTAGNGAAATGGCATTCTTCAGGAATTAAG                         GTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAA-GCTTCTCTTTGGG
genomic: GATGCTTTAGAGAAATGGCATTCTTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
EST: gi|164009508|gb|ES198624.1|ES198624
EST:     GCTTTAGAGAAATGGCATTCTTCAGGAATTAAG                         GTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
genomic: GCTTTAGAGAAATGGCATTCTTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
EST: gi|164171280|gb|ES148604.1|ES148604
EST:     TTCAGGAATTAAG                         GTTTACATATATTCTAG-GGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
genomic: TTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
EST: gi|124720224|gb|EH811626.1|EH811626
EST:     CTTCAGGAATTAAG                         GTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
genomic: CTTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
EST: gi|86088072|gb|DR383831.1|DR383831
EST:     TCGAGGATGTAGCAGATGCTTTAGAGAAATGGCATTCTTCAGGAATTAAG                         GTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
genomic: TTGAGGATGTAGCAGATGCTTTAGAGAAATGGCATTCTTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
EST: gi|164176435|gb|ES054609.1|ES054609
EST:     GATGCTTTAGAGAAATGGCATTCTTCAGGAATTAAG                         GTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG
genomic: GATGCTTTAGAGAAATGGCATTCTTCAGGAATTAAGgtatgttcat ... atgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttttaaagaaatgacatttttttcacaggtctaatggttttcatgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGGAACACAGACTATGGAGATCTGAGAAAGTATATATCTGGCTTTTTCGACA
                               gtctaat  putative branch site (score: 3)
                                        ttttcat  putative PPT
     ttaaagaaatgacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcatgtagcttttaaagaaatgacatttttttcacaggtctaatggttttcatgcgaatagGTTTACATATATTCTAGCGGTAGTCGATTAGCGCAAAAGCTTCTCTTTGGGAACACAGACTATGGAGATCTGAGAAAGTATATATCTGGCTTTTTCGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC