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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctgcagaaagtcagcagtagaatattgtcttctctaattaaggtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA

Basic information

species Oryza sativa
transcript LOC_Os01g46510.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G824843_T02 (Zea mays), 3'ss of exon 1
-----tatctgcagaaagtcagcagtagaatattgtcttctctaattaaggtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA
     |  |   |||||   |      |||  || | | |  || |  | || | | |||    ||  ||  ||||     | ||   ||| | |||   | ||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| |
ttgtttgaccatagaaataaaaacactgaactttctgtccattagtataagt-tcggcag----cagaaagtcttctgtctagtgtaatggctatgatatttcagGTTATTGGATTGCATGGTGGTGCTTTACTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTTTGACAGCAACAGCTATATCAACTGTTCAATCGA
















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|58664662|gb|CK053348.1|CK053348
EST:     AGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: AGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|29626669|gb|CB631680.1|CB631680
EST:     ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCAT
genomic: ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCAT
EST: gi|58658218|gb|CK046898.1|CK046898
EST:     ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|86889062|gb|CI314678.1|CI314678
EST:     GCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: GCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|25804329|gb|CA760290.1|CA760290
EST:     ATGGAACAGCACATGTTNTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTNTGCTTGGTGTCACATACCGTACATCT
genomic: ATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
EST: gi|58656516|gb|CK045196.1|CK045196
EST:     AACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCG                         GTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT
genomic: AACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCT

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: 47 (upstream exon), 70 (downstream exon)
Score: 13

AGCTAGTGCTGCTTCTGCAGCCACAGTACAAGTGCGCATCTTATTAGATGATGGAACAGCACATGTTTTGCAGCGATCCATTGATGGCCGCAGTGAACCGgttggcaatc ... gaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttgtcagtactcaataatgcttcaagaaaatgatgtggttgtgaccgtgcagGTAATTGGATTGCATGGTGGTGCTTTGCTTGGTGTCACATACCGTACATCTCGTAGAATCAGTCCTGTGACAGCAACAGCTATATCAACTGTTCAATCTA
             tcaataat  TA-rich tract