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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGCAGTGAGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgtttactctgcttattggatgattacttttgtgtcctgtgttttatacaaactcttttctaatgtcttagtcgagttttataaagaagcttgcagtcattaaaagctagctctaggttactgatgtctcatttctgctttggatttatttggtacag

Basic information

species Arabidopsis thaliana
transcript AT5G04740.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G04740.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0147g00220.t01 (Vitis vinifera), 5'ss of exon 6
GAATGCAGTGAGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgtt-tactctgcttattggatgattacttttgtgtcctgtgttttatacaaactcttttctaatgtcttagtcgagttttataaagaagcttgcagtcattaaaagctagctctaggttactgatgtctcatttctgctttggatttatttggtacag
|| | ||||||||||||||| ||||||||  |||||||||| || ||||| ||||||||||| || || |       | ||| |     || |||  | |||| |  ||| |     ||| |  || || |         | | ||| | | |  |||  ||  || |                                                       
GAGTCCAGTGAGCAACTTGCTATGGGTGAAGCTTTTGGAATCAAAGCTCCAGAAAAGAAGgtgatattgttaaacattcattaggcttatattttcttctccttttgtttctgtttgctcctaactgatct---------gctgtattatggactttgatgtttttgat------------------------------------------------------
















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|124912677|gb|EH986672.1|EH986672
EST:     AATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: AATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
EST: gi|86082088|gb|DR377847.1|DR377847
EST:     AGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: AGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
EST: gi|164060850|gb|EL967300.1|EL967300
EST:     TGGGTGAGTACTTTTGGAAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: TGGGTGAG-ACTTTTGG-AATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
EST: gi|164129830|gb|EL977746.1|EL977746
EST:     TGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: TGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
EST: gi|164163520|gb|EL968307.1|EL968307
EST:     TGGGTGAGAC-TTTGGAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: TGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
EST: gi|125010476|gb|EL082745.1|EL082745
EST:     AATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: AATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
EST: gi|124733233|gb|EH824635.1|EH824635
EST:     TGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTG
genomic: TGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTG
EST: gi|164169079|gb|ES199945.1|ES199945
EST:     GAGACTTTTGGAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAG
genomic: GAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAG
EST: gi|86079610|gb|DR375367.1|DR375367
EST:     AGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAG                         ATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG
genomic: AGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgttta ... tttggtacagATTGATGTCGATATCGCAACTCATATACATGTGAAAGAAGATGGACCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGCAGTGAGCAACTTGCAATGGGTGAGACTTTTGGAATAAAGGCTCCCGAAAAGAAGgtaatgtttactctgcttattggatgattacttttgtgtcctgtgttttatacaaactcttttctaatgtcttagtcgagttttataaagaagcttgcagtcattaaaagctagctctaggttactgatgtctcatttctgctttggatttatttggtacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG