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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctcttcaagcatgttttttttctctcatgtgatggttaattaaagtgtttttgctttgagcttcagttattcatatctatgatgcgatgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAAACTCTGAG

Basic information

species Oryza sativa
transcript LOC_Os08g21660.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g21660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
gttctcttcaagcatgttttttttctctcatgtgatggttaattaa--agtgtttttgctttgagcttcagttattcatatctatgatgcgatgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAA-ACTCTGAG
  | | |  || | | ||| | ||   |  ||   | ||| ||  |  |     |||| |||   ||     | | ||| | | |  |  ||| |||   || ||||| ||||| ||||||||||| |||||||||||||| ||||||||||| |||||||||| ||||||||| || |   ||||   | ||  |  | || 
-ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaattatgtccatgttttttctctgatcttat-tagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA-

upper sequence: LOC_Os08g21660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 6
gttctcttcaagcatgttttttttctctcatgtgatggttaattaaagtgtttttgctttgagcttcagttattc-atatctatgatgcgatgtta--aacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAAACTCTGAG
     |||     ||   |||| |||  | |      |||| ||  |   |||     ||    || | | | || || |  ||  |   || |||  |  |||||||| ||||||||||||||||||||||||||| |||| |||||||||||||||||||| | |||||| || || |   ||||     |||  || |||
-catgctttgtagataccttttctcttgcgttctggagttatttttaaattttagaagtt--tttttactaactccatgttcattcttttatcttattattagCTTTTCAAGTGGTGGTGAAGATGGATATGTAAGGTTGCATCATTTTGATTCTGACTACTTTAGCATCAAAATGTAGATAAAGAACAGACGAA--TCAGAG

upper sequence: LOC_Os08g21660.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 6
----gttctcttcaagcatgttttttttctctcatgtgatggttaattaaagtgtttttgctt-tgagcttcagttat-tcatatctatgatgcgatgttaaa--cagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAAACTCTGAG
     ||  |  ||      ||||  ||   | |    ||  | |  | | | | |||||  | || | ||  | | | |||      |  ||  ||||  |   ||| || || ||||| |||||||| || || || |||||||| |||||||| || ||||||||||||||||||||||| |    ||     ||||  ||    
gtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC

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|29637698|gb|CB642707.1|CB642707
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88259051|gb|CI363344.1|CI363344
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATTTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|89174599|gb|CI110797.1|CI110797
EST:     GGCCCTTTTGGACCCATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGGAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86428041|gb|CI073138.1|CI073138
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTC--GTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86539171|gb|CI179377.1|CI179377
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|427350|gb|D23414.1|D23414
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         -TTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88552964|gb|CI483028.1|CI483028
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88534415|gb|CI463136.1|CI463136
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88983105|gb|CI020669.1|CI020669
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|87015288|gb|CI275478.1|CI275478
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86866716|gb|CI343538.1|CI343538
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86255807|gb|CI066870.1|CI066870
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|89193673|gb|CI116306.1|CI116306
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88296843|gb|CI540195.1|CI540195
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88557329|gb|CI487726.1|CI487726
EST:     GGCCATTGTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86896321|gb|CI330184.1|CI330184
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|15849426|gb|BI797702.1|BI797702
EST:     CATTTTGGACCCATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: CATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86494802|gb|CI137435.1|CI137435
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|10794823|gb|AU108789.1|AU108789
EST:     GGCCATTTTGGNCCAATTAACGCGCTGGCATTTAANCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88978627|gb|CI384968.1|CI384968
EST:     TTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: TTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86495775|gb|CI138408.1|CI138408
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|218499018|gb|FG959220.1|FG959220
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88222839|gb|CI220690.1|CI220690
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86419096|gb|CI053897.1|CI053897
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|33794412|gb|CF323090.1|CF323090
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|86419296|gb|CI054097.1|CI054097
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
EST: gi|88549198|gb|CI479063.1|CI479063
EST:     GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAG                         CTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC
genomic: GGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattct ... tgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgtttttgctttgagcttcagttattcatatctatgatgcgatgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAAACTCTGAG
                        ttattcatatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctcttcaagcatgttttttttctctcatgtgatggttaattaaagtgtttttgctttgagcttcagttattcatatctatgatgcgatgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAAACTCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - -aagcatg
- - - - - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgc