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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGCATCTGCCGTTTGCCCTAGTGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacattctttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtgttgttatttgttcgttcag

Basic information

species Oryza sativa
transcript LOC_Os11g03900.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G180155_T01 (Zea mays), 5'ss of exon 4
-AGACGCATCTGCCGTTTGCCCTAGTGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacattctttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtgttgttatttgttcgttcag
    |||  |||| || ||||| |||||||| ||||| || ||||||||||| ||||| ||    |||||||||||||||||||||||||| || |||||||||||    || | | | |    |  ||   |||   ||      || |   ||   || |   ||     ||||  |||            || |||| ||| || ||||||
CCACCGCG-CTGCTGTATGCCCCAGTGGATCCTGCAGAGTCATTGAAGTTCCGGAGGTTGCATGTTGTCTCCAGCCAGTGATTAACATAATCCCATTACAGgtttgt---ttgtctaattaagcttgttctgtca---tctgtttttttttggtacagttcactgttcactgaacagattc------------tgctgtttttttttggttcag

upper sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G005849_T02 (Zea mays), 5'ss of exon 10
AGACGCATCTGCCGTTTGCCCTAG---TGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacattctttgaattgtttaatttcatcaaattccagaacttctacttatgctttatcatttgtgaaacaatttcatttactgagtgtgttgttatttgttcg-ttcag
    ||  | || || ||||||||   ||| || ||||| || |||||||||||| |||| || |||||||||||||||||||| ||||||||||| |||||||||||       | | |   | ||  |||      | |||    | ||   || |  |||  ||  | |    ||||||    |||||| |   ||||||||| || | |||||
---TGCCGCGGCTGTGTGCCCTAGCGGTGGGTCGTGCAGAGTCATTGAAGTTCCACAGGTTGCAGACTGTCTCCAGCCAGTGATCAACATAATTCCATTACAGgtttg-------tctaa---gcttggtttgtgtggagtccgt--cctcagattttaattttccaccttt----caattt----tactga-taaattgttatttctttggttcag
















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|88220725|gb|CI220285.1|CI220285
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86424995|gb|CI070092.1|CI070092
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|33681120|gb|CF309359.1|CF309359
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88479293|gb|CI416564.1|CI416564
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|33822256|gb|CF336942.1|CF336942
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88263345|gb|CI367119.1|CI367119
EST:     CAGAGTTCGCTGACTGTCTCCAGGCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTGTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88320801|gb|CI527953.1|CI527953
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|58669396|gb|CK058082.1|CK058082
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|33689236|gb|CF317475.1|CF317475
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|27548069|gb|CA766086.2|CA766086
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88267139|gb|CI379074.1|CI379074
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCCTTACAC                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88997627|gb|CI390262.1|CI390262
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|112785889|gb|EE591621.1|EE591621
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88490264|gb|CI427536.1|CI427536
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88263330|gb|CI367104.1|CI367104
EST:     CAGAGGTCGCTGACTGTCTCCAGGCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|38479057|gb|CF963190.1|CF963190
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86430525|gb|CI082948.1|CI082948
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88483553|gb|CI420824.1|CI420824
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|86489453|gb|CI132086.1|CI132086
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
EST: gi|88226050|gb|CI225966.1|CI225966
EST:     CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAG                         CTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA
genomic: CAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCA

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: 74 (upstream exon), 57 (downstream exon)
Score: 9

AGACGCATCTGCCGTTTGCCCTAGTGGATCTTGCAGGGTTATTGAAGTTCCAGAGGTCGCTGACTGTCTCCAGCCAGTGATTAACATAATTCCGTTACAGgtttgcacat ... gttcgttcagCTGCTCGCATACCATCTGACAGTTCTTCGAGGATTTGATGTTGATCAACCAAGGAATCTGGCAAAGAGTGTGACTACCCAATGAGTAGGGGGTTCTATCA




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