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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctattcctgaattcttatgtccttcataccccttgttgcaagaccagatatacacagggtcctgtatattgagtattcttatcttctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGGCACATAACTCGAATAGCTAATAAGCTTATTCAACTGGGAAATAGCAACA

Basic information

species Oryza sativa
transcript LOC_Os05g51490.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G812498_T01 (Zea mays), 3'ss of exon 3
gtaa-tctattcctgaattcttatgtccttcataccccttgttgcaagaccagatatacacagggtcctgtatattgagtattcttatcttctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGGCACATAACTCGAATAGCTAATAAGCTTATTCAACTGGGAAATAGCAACA
|||| |||||| ||| || ||| |   |||       ||  | ||  | | |  |    |         |||| |||| ||| |    ||| | | || |||||||||||| ||| |||||||| |  ||||||| ||||||||||||||||||||||||||||||||| |||||||| |||||| | |||||||| ||||
gtaaatctatttctggatacttgtcaacttggc-tttctcttggctgggctatgtcgcta---------gtattttgattatgc----cttgtgtttgtagCCAACATTACCATCAGAAGGGAAAGAACCTCCAAGAATTGGGAATATTGGGCACATAACTCGAATAGCGAATAAGCTCATTCAATTTGGAAATAGTAACA
















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|58611996|gb|CK039708.1|CK039708
EST:     AAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACA                         CCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGG
genomic: AAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACAgtaatctatt ... ctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGG
EST: gi|58611304|gb|CK039016.1|CK039016
EST:     AATTCTTGCTGCTGAAAGAAGTTCCTCCCTGGTCAACAGAATCTAACACA                         CCAACATTACTATCTG
genomic: AATTCTTGCTGCTGAAAGAAGTTCCTCCCTG-TCAACAGAATCTAACACAgtaatctatt ... ctatgtgcagCCAACATTACTATCTG
EST: gi|58653975|gb|CK042655.1|CK042655
EST:     AAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACA                         CCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGG
genomic: AAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACAgtaatctatt ... ctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGG
EST: gi|58689163|gb|CK077850.1|CK077850
EST:     AAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACA                         CCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGG
genomic: AAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACAgtaatctatt ... ctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGG

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: 66 (upstream exon), 75 (downstream exon)
Score: 32

TAGATCCCAGCTGATTGACCATGCCCTTAATGAATGCAATCTTGTTGGCAAAATTCTTGCTGCTGAAAGAAGTTCCTCCCTGTCAACAGAATCTAACACAgtaatctatt ... ctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGGCACATAACTCGAATAGCTAATAAGCTTATTCAACTGGGAAATAGCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaccagatatacacagggtcctgtatattgagtattcttatcttctatgtgcagCCAACATTACTATCTGAAGGGAAGGTGCCTCCAAAAATTGGGAATATTGGGCACATAACTCGAATAGCTAATAAGCTTATTCAACTGGGAAATAGCAACA
                                 tattcttatcttct  CT-rich tract
                                 tattcttat  TA-rich tract