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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgcttattttggttactgaaatttattagccatgactcatgatatagtttttaatcaaaagttgttccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCTCTTCTAGAAACATTAGACAAAGTGATTTTGAAG

Basic information

species Arabidopsis thaliana
transcript AT3G23700.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23700.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0062g00830.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtgagttgcttattttggttactgaaatttattagccatgactcatgatatagtttttaatcaaaagttgttccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCTCTTCTAGAAACATTAGACAAAGTGATTTTGAAG
                          ||   || || |||   ||  || | ||| |     ||| |  |   |   ||||| ||| |  | |||    ||||||| |  ||||||||||||||| | || || |||||||| ||||| ||||| ||| ||||||| ||||||||||| |||    ||
tttgtgcatttggaatttagctaaactggaatggtt-tttaaattggtgtagtttttctttaatggca-acatttgggttttgaattagtacttg----aatgcagGGTAAAATCAAGGATTACATTGTCAATTAAACAACTGGAAGAAGATCCACTTTTAGAAACTTTAGACAAAGTAATTCCTCAG
















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|116466810|gb|EG509402.1|EG509402
EST:     CGGG-TATAGTCACGAATATTGACAA                         AGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCTCT
genomic: CGGGTTATAGTCACGAATATTGACAAgtgagttgct ... tccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCTCT
EST: gi|125247411|gb|EL261496.1|EL261496
EST:     GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAA                         AGAGAAATCAAGGATTACACTATCCATCAAACAA
genomic: GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAAgtgagttgct ... tccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAA
EST: gi|125270491|gb|EL284576.1|EL284576
EST:     GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAA                         AGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGA
genomic: GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAAgtgagttgct ... tccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGA
EST: gi|124861690|gb|EH946127.1|EH946127
EST:     GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAA                         AGAGAAATCAAGG
genomic: GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAAgtgagttgct ... tccaatgcagAGAGAAATCAAGG
EST: gi|125251487|gb|EL265572.1|EL265572
EST:     GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAA                         AGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCT
genomic: GTACTACGCGATGGTGACGAGGTTCGGGTTATAGTCACGAATATTGACAAgtgagttgct ... tccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattagccatgactcatgatatagtttttaatcaaaagttgttccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCTCTTCTAGAAACATTAGACAAAGTGATTTTGAAG
                            ttttaat  putative branch site (score: 3)
                                         ttgttcc  putative PPT
                  atgatatagtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgcttattttggttactgaaatttattagccatgactcatgatatagtttttaatcaaaagttgttccaatgcagAGAGAAATCAAGGATTACACTATCCATCAAACAACTAGAAGATGATCCTCTTCTAGAAACATTAGACAAAGTGATTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG