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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagagctaactccttttccttcattacattcttgtttgattgttctgtttccataattttacaattcggaaactgttcaacagttccttgtcgga...

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 6
TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagagctaactc-----cttttccttcattacattcttgtttgattgttctgtttccataattttacaattcggaaactgttcaacagttccttgtcgga
||||||||||| |  ||||| ||||||||||||||  |||||||||||||||  |||||||| ||||||||||| ||||| |||||||| |||||||||||| |||| |  |  ||       || || | |||  ||| ||||||  || |   |||||  ||| ||||     |   ||  | |   | |  |  |  ||   
TGGTTAGTTGGGATGCAATACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCTCCGTGGGCCATTGATTCTTGGGGACTGGgtgagcataaatctcttgatggtttctcatgcatggcatgcttgtt--atggaattgttt--atattttttttggttacaatatatgggagaagttgtgttcta-

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 6
TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagagctaactc----------cttttccttcattacattcttgtttgattgttctgtttccataattttacaattcggaaactgttcaacagttccttgtcgga
||||||||||||||||| || ||||||||||||||  |||||||||||||||  |||||||| |||||||| |||||||| |||||||| |||||||| ||| |||  |  ||||||          ||  || | ||| |||| ||||||  || ||| |  ||  ||| ||||    |  | ||| |      | | ||||       
TGGTTAGTTGGAACACAGTACAAGCCAATGGAGCTGTCAAAGTCAGATTGGGCTTCAATTAGAAAATCACCCCCATGGGCCATTGATTCTTGGGGACTAGgtgagcgtaaataactcttaatggttcctcctcatgcatgacatgcttgtt--atggttgtacttatata-tttttttttgagtaaagtacatttccggtcct-------

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G38740.1 (Glycine max), 5'ss of exon 6
TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagagctaactccttttccttcattacattcttgtttgattgttctgtttccataattt--tacaattcggaaactgttcaacagttccttgtcgga
||| | |||||| ||||||| || ||||||||| |  |||| ||||| ||||   |||||| ||| || ||||||||||| |||||||| |||||  |||||| |  |   |   | | |||   | ||            |      |  ||||  ||  |    || ||  ||| |||  |     | ||   ||||   
TGGCTTGTTGGATCACAATACAAACCAATGGAGTTGGCAAAATCAGACTGGGATGCAATTAAGAAGTCTCCTCCATGGGCCATTGATTCTTGGGGCATGGgtatgttgttttctgttccttttgatgatagttcatagtgatagcaaattggtttatatggtgcaatagaacacgggaacaatctgctatttttgtgtct--

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 5'ss of exon 6
TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaa-gcagagctaactcctt-ttccttc---------attacattcttgtttgattgttctgtttccataattttacaattcggaaactgttcaacagttccttgtcgga--
||| |||| |||||||| || |||||||||||  |    ||||| ||||||||  | ||||||||||| || |||||||| |||||||| |||||| | ||||  | ||   | |  ||||  |  |||         |||| || ||   | ||   ||      |   | |  ||   ||     |  |  |   | |||||| |  ||  
TGGCTAGTGGGAACACAGTACAAGCCAATGGAAATGGTCAAGTCTGATTGGGTTGCTATTAGGAAATCTCCACCATGGGCCATTGATTCGTGGGGATTAGgtactgtagtttttatgccttactaattctcaatggagattatatgctc-ctcgacccttagtgcacttgagtgctattctttcactaaagccctttacttccttttttgaag

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|29623603|gb|CB628614.1|CB628614
EST:     GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGG                         GGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
genomic: GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
EST: gi|58662163|gb|CK050843.1|CK050843
EST:     GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGG                         GGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
genomic: GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
EST: gi|88397102|gb|CI593314.1|CI593314
EST:     GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGG                         GGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGATAACCAGGACAGAGG
genomic: GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
EST: gi|29622867|gb|CB627878.1|CB627878
EST:     GTGTCAATTAGGAAATCACCTCCATGGGGCA-TTGATTCCTGGGGACTGG                         GGTGGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACC
genomic: GTGTCAATTAGGAAATCACCTCCATGGG-CAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTG-TTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACC
EST: gi|58684299|gb|CK072986.1|CK072986
EST:     GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGG                         GGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
genomic: GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
EST: gi|29623070|gb|CB628081.1|CB628081
EST:     GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGNGGACTGG                         GGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG
genomic: GGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGG

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: 75 (upstream exon), 74 (downstream exon)
Score: 22

TGGTTAGTTGGAACACAATATAAGCCAATGGAGCTAACAAAGTCAGATTGGGTGTCAATTAGGAAATCACCTCCATGGGCAATTGATTCCTGGGGACTGGgtaagcagag ... ctcattgcagGGTGTTTAATTTATGAGCTCTTTTCTGGTGCAAAGCTAACCAGGACAGAGGACCTTCGGAACACTGCTTCAATCCCAAAG




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