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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggaccacttcatcgttttccactagttgtgtttttttgtttaagttgtggtgctactgtctatttgtaatcgttttgggttatctgtctcatttgtattatcctgtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g55590.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G460078_T01 (Zea mays), 5'ss of exon 13
GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggacca--cttcatcgttttccac---tagttgtgtttttttgttt------------aagttgtggtgctactgtctatttgtaatcgttttgggttatctgt---ctcatttgtattatcctgtgtag
|| || |||||||| || |||||||| || ||||||||||| |||||||||||||||||||| || |||||||| ||||||||||| || |||||| | ||   || ||     | |||      || |||  || |  ||            |  | |||||| ||||| |||   |     | || || ||   |||   |||||||| |||| | |||| ||
GTCACCGCAGAATCTTTCATTGATGGAGGATTCTTCAAGACAGGTGATACAGTAACTGTAGATGAGGAAGGATACTTCATAATTTTGGGACgtaagtaacagtttttatgcacatgcacgcacgcttatgtccttctagttgctgttttcatcacctcgtggtgttactgccta---gggtcagcttcggtttgcttgtagcctcatttgcattaccttgtgcag

upper sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA08G21840.1 (Glycine max), 5'ss of exon 13
GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggaccacttcatcgttttccactagttgtgtttttttgtttaagttgtggtgctactgtctatttgtaatcgttttgggttatctgtctcatttgtattatcctgtgtag
|  ||    |||||||||| ||||| ||| |||||||||||||| ||| |||| |||  ||| || || ||||||||||| ||| |||| ||||||||  | || ||  |||  || |   ||   |  | |||||   ||||     |     |  | |||      | | |  ||  | ||     |  ||||          
GCAACAAAGGAATCATTTACTGATGATGGATTCTTCAAGACTGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaagga--aatttat-atttctcaatgtatgctgtcatatgttttc-ttgtaagagtcagaaccttgtgtgcagcctgtagcataattctcatgccttaatta----------

upper sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G02180.1 (Glycine max), 5'ss of exon 13
GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggaccacttcatcgttttccactagt----tgtgtttttttgtttaagttgtggtgctactgtctatttgtaat-cgttttgggttatctgtctcatttgtattatcctgtgtag
|| ||    |||||||||| ||||| ||| ||||| |||||||| ||| |||| |||  ||| || || ||||||||||| ||| |||| ||||||||    |  ||   ||  |  |  |    | |||||| | ||   |||     |  |     |    ||||      || |  |  | |   | |                   
GTAACGAAGGAATCATTTACTGATGATGGATTCTTTAAGACTGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaatttatatttcttatctatgctgtcatatgttttctcgtaagagtcagaatcttgagtgccgcctgtagcataattcgcatgctttaattaa-------------------

upper sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 5'ss of exon 13
GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggaccacttcatcgttt-tccactagttgtgtttttttgtttaagttgtggtgctactgtctatttgtaatcgttttgggttatctgtct-catttgtattatcctgtgtag
|| |||   ||||||||||||||||| ||||||||||||||||||||| | || |  || || || || ||||| | ||| || || || |||||| |   ||  ||| | | | ||  |       |  |    |||  ||    ||    | |  | | || | |   ||  |   ||| | |    |||               
GTAACTAAGGAATCATTTATTGATGGCGGGTTCTTCAAGACTGGTGATGCTGTTAAAGTGGATGACGATGGATACTACATCATCTTGGGACgtaagtagacctagatcctatatgcatgaaccaacatggtcctattatttttaaatgg-gttattaactcgtcaccaaattttgccctctatatgtggttg---------------

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|10852848|gb|AT003358.1|AT003358
EST:     TGGTGATACAGTACCTGTAGNCGATGAAGGATATTTCAT-ATTTTAGGGC                         GCNCAAATGCTGCCATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
genomic: TGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggacca ... tcctgtgtagGCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
EST: gi|89185889|gb|CI047758.1|CI047758
EST:     TATTTCATAATTTTAGGGC                         GCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
genomic: TATTTCATAATTTTAGGGCgtaaggacca ... tcctgtgtagGCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
EST: gi|29689640|gb|CB685915.1|CB685915
EST:     TGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGC                         GCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
genomic: TGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggacca ... tcctgtgtagGCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
EST: gi|58603395|gb|CK013923.1|CK013923
EST:     TGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGC                         GCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG
genomic: TGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggacca ... tcctgtgtagGCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAG

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), 38 (downstream exon)
Score: 33

GTTACTGCAGAATCATTTATTGATGGTGGGTTCTTCAAGACTGGTGATACAGTAACTGTAGACGATGAAGGATATTTCATAATTTTAGGGCgtaaggacca ... tcctgtgtagGCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG




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