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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttgtcaaactgtgattgtttcaggattatgaataaaccagctctttatatcctaaatggttttttgtttctgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACCACTCACGAAGGTCAACAACTTGATATTTGGGCGTACTTGGGTTGATTCT

Basic information

species Oryza sativa
transcript LOC_Os03g16690.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------------gtaattttgtcaaactgtgattgtttcaggattatgaat--aaaccagctctttatatcctaaatggttttttgtttctgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACCACTCACGAAGGTCAACAACTTGATATTTGGGCGTACTTGGGTTGATTCT
                                                       | |||     ||| ||  |   |||  | |   |||||    ||||| | ||   ||||    ||   | |  ||||    |||||||||||||||| ||||||| || || ||||||  | |||| ||||| |||||||| || ||||| |||||| |||||||||||||||||||||||||||||
gttaattgttagaattgtatttctttcttggagatctgtatggcttaaaaatattttattggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGTACTTGGGTTGATTCT

upper sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------gtaattttgtcaaactgtgattgtttc-aggattatgaataaaccagctctttatatc-------ctaaatggttttttgt---ttctgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACCACTCACGAAGGTCAACAACTTGATATTTGGGCGTACTTGGGTTGATTCT
                                                                    ||||    | |||  |  |   |||  | |  |  |     ||||  | | || |||       ||||    | |  | |   |||    |||||||||| ||||| |||| || || || ||||||  | |||| ||||| |||||||| || ||||| |||||| ||||||||||||| |||||||||||||||
gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT
















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|88694164|gb|CI738202.1|CI738202
EST:     TTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAG                         GACTAGAGTGTCACTTAAGAAG
genomic: TTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAGgtaattttgt ... tgcatcacagGACTAGAGTGTCACTTAAGAAG
EST: gi|29618292|gb|CB623304.1|CB623304
EST:     TTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAG                         GACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACC
genomic: TTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAGgtaattttgt ... tgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACC
EST: gi|33380676|gb|CF196019.1|CF196019
EST:     TTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAG                         GACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACC
genomic: TTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAGgtaattttgt ... tgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACC

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), 75 (downstream exon)
Score: 53

GTGCCGCTCACTGTGAAAATGCACATTTTACATATGACATCACCTCCAAGTTGAAGACCAAATTCTTGGGGAACTCTCTGGAAGTTTATCCACTTGGAAGgtaattttgt ... tgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACCACTCACGAAGGTCAACAACTTGATATTTGGGCGTACTTGGGTTGATTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgaataaaccagctctttatatcctaaatggttttttgtttctgcatcacagGACTAGAGTGTCACTTAAGAAGTCCGGTGTCAAGCTGGAATTGGTACCACCACTCACGAAGGTCAACAACTTGATATTTGGGCGTACTTGGGTTGATTCT
                        tcctaaa  putative branch site (score: 53)
                                  ttttttgtttctgc  putative PPT
                  tttatatcctaaat  TA-rich tract