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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAGTGTTAGTACATACACTGTGAAATCTAATCCACAAGATATCATGGCAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaacttaaatcctaagattgtttttgaatagaagttaaagaaagatgtatcattaatggtttgctttggttag

Basic information

species Arabidopsis thaliana
transcript AT4G01610.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01610.2 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA03G38520.1 (Glycine max), 5'ss of exon 8
TTACAGTGTTAGTACATACACTGTGAAATCTAATCCACAAGATATCATGGCAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaa--taaaacttaaatcctaagattgtttttgaatagaagttaaagaaagatgtatcattaatggtttgctttggttag-----------------------
 || ||||||||| ||||||  || || ||| |||| || ||||||||||| || ||||| |||||||| || ||||||||  | |||||||||||||||||||   ||||||   | ||    | | | ||   ||| |  || | | ||  |  ||  | |||   |          |                        
CTATAGTGTTAGTGCATACAGAGTCAACTCTGATCCCCATGATATCATGGCGGAAGTTTACAAGAATGGGCCAGTTGAAGTTGCATTTACCGTTTATGAGgtaaatgaaaactcttaccc----actctattgcgataaatttttatgcaacttccatggtcaatttctgaaaacccaaaaccatcctatttaaaatttataat
















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|116481390|gb|EG523982.1|EG523982
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTTTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|116483179|gb|EG525771.1|EG525771
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|163990347|gb|ES103099.1|ES103099
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTT-ATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAAC
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAAC
EST: gi|125017774|gb|EL090043.1|EL090043
EST:     TTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: TTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|124745664|gb|EH836476.1|EH836476
EST:     CAGAGATTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAA
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAA
EST: gi|124965841|gb|EL039993.1|EL039993
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAAT
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAAT
EST: gi|164203480|gb|ES044209.1|ES044209
EST:     GAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: GAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|125036597|gb|EL108866.1|EL108866
EST:     CCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: CCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|163997877|gb|ES205387.1|ES205387
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTAGCTCATTACAAATCTGGAGTCTAT
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTT-GCTCATTACAAATCTGGAGTCTAT
EST: gi|125122565|gb|EL169107.1|EL169107
EST:     GAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCCGAC
genomic: GAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|124783405|gb|EH873249.1|EH873249
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAAT
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAAT
EST: gi|124820883|gb|EH905749.1|EH905749
EST:     GTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: GTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|125151406|gb|EL183553.1|EL183553
EST:     GTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: GTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|164008065|gb|ES018831.1|ES018831
EST:     GAGGTTTATAAGAATGGACCTGTTGAAGTCTC-TTTACCGTTTATGAG                         GATTTTGCTCAATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAA
genomic: GAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTC-ATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAA
EST: gi|124973631|gb|EL047243.1|EL047243
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAAC
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAAC
EST: gi|124903975|gb|EH978055.1|EH978055
EST:     TTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAA
genomic: TTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGC-TCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAA
EST: gi|116483180|gb|EG525772.1|EG525772
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|86077484|gb|DR373241.1|DR373241
EST:     CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: CAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|125201827|gb|EL216781.1|EL216781
EST:     CCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
genomic: CCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC
EST: gi|124890872|gb|EH969774.1|EH969774
EST:     GTTGAAGTCTCTTTTACCGTTTATGAG                         GATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTGCTAAC
genomic: GTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaac ... ctttggttagGATTTTGCTCATTACAAATCTGGAGTCTATAAGCACATAACAGGTTCTAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAGTGTTAGTACATACACTGTGAAATCTAATCCACAAGATATCATGGCAGAGGTTTATAAGAATGGACCTGTTGAAGTCTCTTTTACCGTTTATGAGgtaataaaacttaaatcctaagattgtttttgaatagaagttaaagaaagatgtatcattaatggtttgctttggttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG