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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g37180.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 11
ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcag
|| || ||||| || |||||| |||||||||| || |||||||||||||| ||||             || |||    ||   || ||||  | || |||  |  || | ||            |||||||||||     ||||| || |||||
ATTTATCCACCTATTAATGTCCTGCCATCTCTTTCACGATTGATGAAGgtaagat-------------aagttttctgta---tgttttc--agcatttatgttgtagatta------------gttctaagaaccactgaataactcctgcag

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 12
ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcag
|| || ||||| ||||||||| |||||||||| ||||||||||||||||| |||| | |  ||  |||   ||   |||         | ||    |||  | | ||                 ||| |||||||    ||| || || |||||
ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttttctgtatgttttcagcat---------ttat----gttgaaggtta-----------------gttgtaagaaccacttaacaactcctgcag

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G094497_T04 (Zea mays), 5'ss of exon 1
----------------------------------------------------ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcag
                                                    || || ||||| || |||||| |||||||||| || |||||||||||||| ||||             || |||    ||   || ||||  | || |||  |  || | ||            |||||||||||     ||||| || |||||
TACTACCTTGATAGCTTATCTGTGTTGATGTGATGGCATTATATTCTTTCAGATTTATCCACCTATTAATGTCCTGCCATCTCTTTCACGATTGATGAAGgtaagat-------------aagttttctgta---tgttttc--agcatttatgttgtagatta------------gttctaagaaccactgaataactcctgcag

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 11
ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcag--
|| |||||||| ||||||||  |||||||||| || ||||||||||||||| |       || | |||     |  | |    || | | |  |  |||   |    |   | | | | | | ||| |  |  ||  | |   || ||    ||  
ATCTACCCACCTATCAATGTGCTGCCATCTCTGTCGCGATTGATGAAGgtgcggccttatatta-tat---ccttgcgt---ttgttatgaccagcgttttctttatcttcagtatacttattcgtgcccactac-atttttcaagtcacagagtg

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|87038558|gb|CI193180.1|CI193180
EST:     ACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|33684047|gb|CF312286.1|CF312286
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGNTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAA
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGG-TGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAA
EST: gi|24468720|gb|CA305669.1|CA305669
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29665773|gb|CB662048.1|CB662048
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29681070|gb|CB677345.1|CB677345
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|86537237|gb|CI177443.1|CI177443
EST:     ATATACCCACCCATCAATGTCGTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29675288|gb|CB671563.1|CB671563
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29642144|gb|CB647151.1|CB647151
EST:     AGATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: AGATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|58605789|gb|CK033822.1|CK033822
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAG
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAG
EST: gi|89187389|gb|CI047456.1|CI047456
EST:     CCACCCATCAATGTCTNGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: CCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29684019|gb|CB680294.1|CB680294
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29630857|gb|CB635866.1|CB635866
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|88198947|gb|CI198797.1|CI198797
EST:     CCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: CCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29630447|gb|CB635456.1|CB635456
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|218488216|gb|FG965996.1|FG965996
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|58674437|gb|CK063123.1|CK063123
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29678975|gb|CB675250.1|CB675250
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|86536379|gb|CI176585.1|CI176585
EST:     ATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|700311|gb|D46602.1|D46602
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGGTTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAG
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAG
EST: gi|25801982|gb|CA757943.1|CA757943
EST:     AGATATACCCACCCATCAATGTCTTGCCATCCCCCTCTCGATAGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: AGATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|300215980|gb|HO088606.1|HO088606
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|58594202|gb|CF992510.1|CF992510
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGT-CTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|86535166|gb|CI175372.1|CI175372
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|27554550|gb|CA998450.1|CA998450
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29678974|gb|CB675249.1|CB675249
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|58682214|gb|CK070901.1|CK070901
EST:     CTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: CTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29668005|gb|CB664280.1|CB664280
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|58662859|gb|CK051545.1|CK051545
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29617704|gb|CB622716.1|CB622716
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|87024279|gb|CI257020.1|CI257020
EST:     TCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: TCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29684020|gb|CB680295.1|CB680295
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29669855|gb|CB666130.1|CB666130
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|58688525|gb|CK077212.1|CK077212
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|88902578|gb|CI088116.1|CI088116
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|29665772|gb|CB662047.1|CB662047
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
EST: gi|56157325|gb|D41816.2|D41816
EST:     ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC
genomic: ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 56 (downstream exon)
Score: 76

ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattac ... attcttgcagAGTGCTATTGGTGAGGGTATGACCCGTCGAGACCATTCAGATGTGTCTAACCAG




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