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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctctgtctcaagaggtcttttctgctatgatttaccttctgacatttcatttataagttttattttccgtttggcag

Basic information

species Arabidopsis thaliana
transcript AT1G23310.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23310.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S215_28V6.1 (Physcomitrella patens), 5'ss of exon 5
TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctctgtctcaagaggtcttttctgctatgatttaccttctgacatttcatttataagttttattt---tccgtttggcag---------------
 || || ||    ||||| ||||||||||||||||||||||||||    ||| | ||||||    | || |||| | |    ||||||||||| |   |            ||     || |  | |  |||   ||  |  | || |   || | |     |||  |||   |               
CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctcgaactgtctacctttgataactgttctat-tcttgatacgctgaacttcttgtttgtgtccgagtccacttgaaggtctcattctgtcatt

upper sequence: AT1G23310.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: PP1S341_73V6.2 (Physcomitrella patens), 5'ss of exon 5
TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgct-----ctgtc-tcaagaggtc-ttttctgctatgatttaccttctgacatttcatttata--agttttattttccgtttggcag---------
||| || ||    ||||| ||||||||||||||||||||||| ||    ||| | ||||||    | || || | | |   |||||| |||||        ||||  | |  || |  ||||||     ||   || |  |  | |||  || | |  |    || | |  |    | |          
TGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGGGTTGCACAAGTTTTGAATGCCCTCATCCGTGATGAAAAAGATGGAgtaatttctctaactgttattacaagattgttttctttctcgacacacttagtcgc-tttggttgagatcaacgataatgtgaggaatgtaataacctcct
















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|86074112|gb|DR369869.1|DR369869
EST:     NNNGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGTG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|124835509|gb|EH919948.1|EH919948
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGNGATGGG                         ATTCTAGTTCCGGTTCCACAGTA
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTA
EST: gi|124968960|gb|EL042886.1|EL042886
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTAC
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTAC
EST: gi|116482909|gb|EG525501.1|EG525501
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|86074105|gb|DR369862.1|DR369862
EST:     AGGNGTGATGCAAATCTTGAATTGNGT-ATACGCGGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGAATCCACTTTACTCAGCTACCA
genomic: AGGTGTGATGCAAATCTTGAATTGTGTTATACGCGG-TAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCA
EST: gi|116434550|gb|EG477142.1|EG477142
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|124723140|gb|EH814542.1|EH814542
EST:     ATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTCTACTCAGCTACCATATCACTG
genomic: ATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|125245347|gb|EL259432.1|EL259432
EST:     CAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: CAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|301502125|gb|HO207665.1|HO207665
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|124908559|gb|EH982639.1|EH982639
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCA
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCA
EST: gi|124704901|gb|EH796303.1|EH796303
EST:     TGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATC-ACTTTACTCAGCTACCATATCACTG
genomic: TGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|124861150|gb|EH945587.1|EH945587
EST:     GATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCACGCTACCATATCACT
genomic: GATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCA-GCTACCATATCACT
EST: gi|164029950|gb|ES005092.1|ES005092
EST:     AATCTTGAATTAGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTAC
genomic: AATCTTGAATT-GTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTAC
EST: gi|116434562|gb|EG477154.1|EG477154
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|124899875|gb|EH974493.1|EH974493
EST:     AAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|125225778|gb|EL239863.1|EL239863
EST:     TGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATACCACTTTACTCAGCTACCATATCACT
genomic: TGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTAT-CCACTTTACTCAGCTACCATATCACT
EST: gi|125043518|gb|EL115787.1|EL115787
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCA
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCA
EST: gi|116482910|gb|EG525502.1|EG525502
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|86074110|gb|DR369867.1|DR369867
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|86074123|gb|DR369880.1|DR369880
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAANGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|164063684|gb|EL994602.1|EL994602
EST:     AATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTAC
genomic: AATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTAC
EST: gi|125232965|gb|EL247050.1|EL247050
EST:     AAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTAACTCAGCTACCATATCACT
genomic: AAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTA-CTCAGCTACCATATCACT
EST: gi|86074134|gb|DR369891.1|DR369891
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATCACTG
EST: gi|124832595|gb|EH917034.1|EH917034
EST:     AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCA
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCA
EST: gi|86074106|gb|DR369863.1|DR369863
EST:     NNGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG                         ATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATC
genomic: AAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctct ... cgtttggcagATTCTAGTTCCGGTTCCACAGTATCCACTTTACTCAGCTACCATATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctctgtctcaagaggtcttttctgctatgatttaccttctgacatttcatttataagttttattttccgtttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG