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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcatggattactatgattttattgtactgctctgatgtttttgttgtccttaatgttgctttgactgatgtttaatgtggaaattgccttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT

Basic information

species Oryza sativa
transcript LOC_Os02g46510.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 6
gtatttcatggattactatgattttattgtactgctctgatgtttttgttgtccttaatgttgctttgactgatgtttaatgtggaaat-----tgccttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT
||| |  |||||  |   | |||||   | ||||| | | ||| |||             |||  || | |||||||   |||| | ||     || | |  ||||||||||||||||| ||||||||||||| || |||||||||||||| |||||||||||||||||||||||||||||  ||||||||||||||||||| || ||
gtactctatggaccaacctaatttt---ggactgcacagttgtctttacc----------ttgtattaattgatgttccttgtgtacataaatgtgtcattcctgcagGGAGTGTTCTAAGATGTGATGTGACGGGAAAGATTCTTATGAAATGCTTCCTTTCTGGAATGCCTGATCTGAAGCTGGGATTAAATGACAAGATTGGACT

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatttcatggattactatgattttattgtactgctctgatgtttttgttgtccttaatgttgctttgactgatgtttaatgtggaaattgccttctctgc-agGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT
        |  || |   ||  |||  || | |  | ||| ||| |  || |  || || ||||| ||  |||   |   | || |  ||       | |  ||| | |||||| || ||||||||||| |||||| || | ||||| || |||||||| |||||||||||| |||| ||||| || ||||| || || || ||
-------gtaaataat--tgccttttatgaagttttttgaagttgtctttcttgttgat-ttgctgtgtatga--ctggttttgcattttatggaaacggttagGCAATGTTCTTCGGTGTGATGTGACGGGGAAGGTTTTAATGAAATGTTTCCTTTCGGGAATGCCTGATTTGAAGTTGGGGTTGAATGATAAAATTGGTCT

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 6
gtatttcatggattactatgattttattgtactgctctgatgtttttgttgtccttaatgttgctttgactgatgtttaatgtggaaattgccttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT
                             | ||| |||      | | |||| |  ||||    | ||  ||    ||| |  | ||| |    |   || ||| || |||||||| |||||||| ||||| || ||||| ||||| |||||||| ||||||||||||||| |||| ||||| |||||||| || || || ||
------------------------gtgaatgctgttcttggaaatattttgtgc--aatgcatttctgtttg---cttacttagtaaaatttggtgattgtagGTAGCGTTCTACGCTGTGATGTAACTGGAAAAATTCTAATGAAATGCTTCCTCTCTGGAATGCCTGATTTGAAGTTGGGTTTAAATGATAAAATTGGCCT

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatttcatggattactatgattttattgtactgctctgatgtttttgttgtccttaatgttgctttgactgatgtttaatgtggaa--attgccttct-ctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT
     | ||  ||| || |   ||||||| |  ||| | | ||  ||  ||       | |    |   |    ||  ||| | |||   |||  |  |  |||||| | |  | | || ||||| |||||||| |||||| | ||||||||||||||||| |||||||| ||||||||| | ||| | || ||||| || || ||
---acttatttatttcttta--tttattggaaagct-tcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT

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|38469602|gb|CF953733.1|CF953733
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|11565235|gb|AU165871.1|AU165871
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|11565221|gb|AU165857.1|AU165857
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAAGTGCTTC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAA-GTGCTTC
EST: gi|11565225|gb|AU165861.1|AU165861
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTNCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|58672424|gb|CK061110.1|CK061110
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|11025706|gb|AU162307.1|AU162307
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|58679139|gb|CK067826.1|CK067826
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|428998|gb|D25154.1|D25154
EST:     GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|33811253|gb|CF331516.1|CF331516
EST:     ATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: ATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
EST: gi|58684077|gb|CK072764.1|CK072764
EST:     G-TTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAG                         GGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC
genomic: GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCC

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: 49 (upstream exon), 73 (downstream exon)
Score: 34

GTTTTCTTGGACATTGTTGAAAGTGTAAATCTTCTTATGTCTTCTAAAGgtatttcatg ... ttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtccttaatgttgctttgactgatgtttaatgtggaaattgccttctctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT
                                        ttgccttctct  CT-rich tract
                        atgtttaat  TA-rich tract