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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaaccacaacgttctaatgatcgaggctgcaacatgaacgattccaatttagaagttgagattttgatatatgtatattctcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G41540.2 (Glycine max), 5'ss of exon 9
GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgt---aaaaaccacaacgttctaatgatcgaggctgcaacatgaacgattccaat-ttagaagttgagattttgatatatgtatattctcttgcag-------
|| |||||||| || |||||||||||  |||| |||||||| ||||| || ||||||||||| |||||  |||| || |||||||| |||||   |||||| || ||       ||||  |    | ||   | | |   | | | || | |  |    || |  | |||  | |||  || | |        
GCTGGTGGGTTCCCAGAGCCAGAGATCATTCACTACAACCCTAAAGATTTTGACTTTGGGAAAAAGAAATCATTTCCATTCCGTGACCAGgtgataaaaacgaccacacaaatctgatacaattagaaaaggggagggggcaagtgtttgtaactt---ttatagtttattaaaattgactagtacatactat

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G38930.1 (Glycine max), 5'ss of exon 9
GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaaccacaac-gttctaat--gatcgaggctgcaacatgaacgattccaatttagaagttgagattttgatatatgtatattctcttgcag---------------------------------------------------------------------------------------------------
|| |||||||| || |||||||||||  |||| |||||||| ||||| || || |||||||| |||||  |||| || |||||||| ||||| | ||  |||||    | |||  |||  |   || ||  ||   |   |   | |||    | | |  |||| |||  |||||  |||                                                                                                        
GCTGGTGGGTTCCCAGAGCCAGAGATCATTCACTACAACCCTAAAGATTTTGATTTTGGGAAAAAGAAATCATTTCCATTCCGTGACCAGgtgataaaaacaaccacacaaatcagatacaatatgaaaagtgtttgtaacttgtatagtttattaaaaattgacataattatatagtctaatgatatactgaaagtagaaacatattaacaaaagtaaaaactgagtggcgagttctttttacattggcgaaataatgatatttaattttcattattgtgcag

upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv14s0060g00820.t01 (Vitis vinifera), 5'ss of exon 9
GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaac------cacaacgttctaat--gatcgaggctgcaacatgaacgattccaatt--tagaagttgagattttgatatatgtatattctcttgcag
|  |  |||||||| ||||| ||||||||||| |||||||| || |||||||| ||||| || ||||| |||||||| |||||||| ||||||||||       |  ||| | | | |  |||   ||||  | ||  ||   |  | ||   |  ||  |      |||||  |||| ||||  | | || 
GGTGCCGGGTTTCCTGAGCCTGAGATTGTTCACTACAACCCCAAGGAGTTCGATTTTGGCAAAAAGAAAGCATTCCCATTCCGTGACCAGgtaaaaatggacttcctaacatgcaattccgatatgggct-taccagaaaacttctctatcagtgaaaactatttcattgattcatgtctatttccattca-

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|125202968|gb|EL217922.1|EL217922
EST:     CGAAAGGGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATG
EST: gi|124823819|gb|EH908685.1|EH908685
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGG
EST: gi|124867630|gb|EH952067.1|EH952067
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAG
EST: gi|86080119|gb|DR375876.1|DR375876
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|116482238|gb|EG524830.1|EG524830
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|125217142|gb|EL231225.1|EL231225
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAG
EST: gi|125015825|gb|EL088094.1|EL088094
EST:     TCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAAC
genomic: TCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAAC
EST: gi|124917730|gb|EH991604.1|EH991604
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|124893349|gb|EH972251.1|EH972251
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCGG                         CATTTCTTTGCATCGG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGG
EST: gi|125023670|gb|EL095939.1|EL095939
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAG
EST: gi|125168639|gb|EL193184.1|EL193184
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCA
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCA
EST: gi|124810993|gb|EH895859.1|EH895859
EST:     CCTTTCCGTGATCAG                         CATTTCTTTGCTATCGGTTGGAGAAAGCAAAGCATGTCCTCGGATGGAAAC
genomic: CCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGC-ATCGG-TGGAGAAAGCAAAGCATGTCCTCGGATGGAAAC
EST: gi|125270778|gb|EL284863.1|EL284863
EST:     AAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: AAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|124739083|gb|EH830245.1|EH830245
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|125187798|gb|EL202752.1|EL202752
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTG
EST: gi|125281534|gb|EL295619.1|EL295619
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGA
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGA
EST: gi|124834767|gb|EH919206.1|EH919206
EST:     GTAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: G-AAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|125041651|gb|EL113920.1|EL113920
EST:     CGAAAGGGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAAGAAAGCAAAGCATGTCCTCGGATG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGA-GAAAGCAAAGCATGTCCTCGGATG
EST: gi|124931609|gb|EL008951.1|EL008951
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|124917994|gb|EH991868.1|EH991868
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|124908856|gb|EH982936.1|EH982936
EST:     CCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|124741880|gb|EH833042.1|EH833042
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCT
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCT
EST: gi|124828034|gb|EH912900.1|EH912900
EST:     GAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: GAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
EST: gi|86083439|gb|DR379198.1|DR379198
EST:     CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAG                         CATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG
genomic: CGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaacca ... tctcttgcagCATTTCTTTGCATCGGTGGAGAAAGCAAAGCATGTCCTCGGATGGAAACCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGTGGGTTTCCGGAGCCAGAGATTGTTCATTACAACCCGAAAGAGTTCGACTTTGGGAAGAAGAAGGCATTCCCTTTCCGTGATCAGgtaaaaaccacaacgttctaatgatcgaggctgcaacatgaacgattccaatttagaagttgagattttgatatatgtatattctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG