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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaataaccatttcaaatatcaccataaacataccaatctagaagttatcgtgcatgtttacaactaaacatctgccttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATG

Basic information

species Oryza sativa
transcript LOC_Os02g10310.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G093359_T01 (Zea mays), 3'ss of exon 12
gtatggaataaccatttcaaatatcaccataaacataccaatctagaagttatcgtgcatgt---ttacaactaaacatctgccttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATG
||||||||||| |||| ||  | | | |||  ||||   | |   |   |  |  | ||| |   |  ||  |  |||| || | |  |||||||  | || ||  | |||||| |  |||||||||||||||| ||||||||||||||| |||| || || | |||||||||||| ||||||||||| ||||
gtatggaataaacattgcatcttttatcattgacatgtaactgagggtttccttatccatatgaatctcattttgacatgtgacat--ttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATG

upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 12
gtatggaataaccatttcaaatatcaccataaacataccaatctaga-agttatcgtgcatgtttacaactaaacatctgccttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATG
                     |||     |||||||  |||  |  | |   || ||     | |  |  |  |||| |||| |  |||||||  | || ||  | || ||| |||||||||| |||||||| ||||||||||||||| | || || || | |||||||||||||||||||||||| ||||
--------------------gtatgga-gtaaacattgcaacttctatacccatagtatgaatct-tactttgacatgtgccat--ttcagGAACCGGACTCCCTCGGGTGTCTGCTGGAGCTGACATGGAACGGGCAGAAGGAGATACCGGTGGGGAATTTGACCCGCAAGTTCCTAGAAGATGGAGATG
















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|29660372|gb|CB656647.1|CB656647
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88509084|gb|CI436590.1|CI436590
EST:     TGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: TGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86250845|gb|CI007708.1|CI007708
EST:     GGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88907444|gb|CI090238.1|CI090238
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29672587|gb|CB668862.1|CB668862
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29612852|gb|CB617865.1|CB617865
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29657905|gb|CB654180.1|CB654180
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88522799|gb|CI450521.1|CI450521
EST:     CAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGGCTAACATGGAATGGGCAGAA
genomic: CAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAG-CTAACATGGAATGGGCAGAA
EST: gi|86853881|gb|CI329327.1|CI329327
EST:     GAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86599975|gb|CI258315.1|CI258315
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88968670|gb|CI098862.1|CI098862
EST:     CACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: CACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29671043|gb|CB667318.1|CB667318
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86428798|gb|CI075479.1|CI075479
EST:     GGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|89163120|gb|CI100010.1|CI100010
EST:     TAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: TAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|55409338|gb|CV721714.1|CV721714
EST:     CTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: CTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|117232667|gb|CT861058.1|CT861058
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29637362|gb|CB642371.1|CB642371
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86839226|gb|CI331496.1|CI331496
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|14981127|gb|BI305818.1|BI305818
EST:     GCAATCTGAGACC-GGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88266268|gb|CI377170.1|CI377170
EST:     ATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: ATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88420084|gb|CI513765.1|CI513765
EST:     ACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: ACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88904130|gb|CI006363.1|CI006363
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29672144|gb|CB668419.1|CB668419
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88905999|gb|CI089585.1|CI089585
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29636552|gb|CB641561.1|CB641561
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29636597|gb|CB641606.1|CB641606
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86840389|gb|CI342574.1|CI342574
EST:     ACACTAACCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: ACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86496229|gb|CI138862.1|CI138862
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|29664840|gb|CB661115.1|CB661115
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88251258|gb|CI349686.1|CI349686
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTTGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88223961|gb|CI223810.1|CI223810
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|86433902|gb|CI094245.1|CI094245
EST:     GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCCAACATGGAATGGGCAGAAG
genomic: GCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|88259120|gb|CI363413.1|CI363413
EST:     ATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
genomic: ATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAG
EST: gi|27548667|gb|CA766758.2|CA766758
EST:     CAATCTGAGACCAGGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT                         GAGACAGAATCTTTGGGGATGNTTGC
genomic: CAATCTGAGACCAGGGG-ATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaata ... cttctttcagGAGACAGAATCTTTGGG-ATGTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaatctagaagttatcgtgcatgtttacaactaaacatctgccttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATG
                               aactaaa  putative branch site (score: 2)
                                      catctgccttctttc  CT-rich tract
           aagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaataaccatttcaaatatcaccataaacataccaatctagaagttatcgtgcatgtttacaactaaacatctgccttctttcagGAGACAGAATCTTTGGGATGTTTGCTGGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG