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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGACGGCTTTCCGAGGAGGAATTGATGAATCAGTTGCCCACATTTTTGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtactaatacagtaatactgtagctcttgtcatggtagatttcttctgtttctcatagtgcttttttatttcactgaaattttggtgctatgagga...

Basic information

species Oryza sativa
transcript LOC_Os04g42840.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42840.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G052078_T02 (Zea mays), 5'ss of exon 20
TGTTGGACGGCTTTCCGAGGAGGAATTGATGAATCAGTTGCCCACATTTTTGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtactaatacagtaatactgtagctcttgtcatggtagatttcttctgtttctcatagtgcttttttatttcactgaaattttggtgctatgagga---------------------------
||||||||| |||||  | |||||||||||   ||| ||||| |||||| |||||||| | |||||||||||||  |||||||| || ||||| ||||||||  |||| |  | | |     ||     | |      |||| |  |  |  ||||| |||     ||   |||||| | | |  ||| |   ||||                              
TGTTGGACGCCTTTCTCAAGAGGAATTGATTGTTCAATTGCCTACATTTCTGCCAGCATTATTTGATGCTTTTAACAACCAAAGTCCAGATGTCCGAAAGgtcagtaccatcatattttccttgctttgcattattctgtaggtaccgaccttttcttata---tcttgaaatttca-taatacattgctctaatgacttatccttgtcaaattttttttactctag
















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|29626001|gb|CB631012.1|CB631012
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|38478559|gb|CF962692.1|CF962692
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|58682357|gb|CK071044.1|CK071044
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCGAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|14981910|gb|BI306588.1|BI306588
EST:     GTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: GTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|88372765|gb|CI612693.1|CI612693
EST:     TGGCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTGTTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
EST: gi|86902991|gb|CI324461.1|CI324461
EST:     TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAG                         ACTGTTGTATTCTTCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC
genomic: TGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTC

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: 73 (upstream exon), 47 (downstream exon)
Score: 6

TGTTGGACGGCTTTCCGAGGAGGAATTGATGAATCAGTTGCCCACATTTTTGCCAGCACTGTTTGATGCTTTTAGTAACCAAAGCCCTGATGTTCGAAAGgtaggtacta ... atatttttagACTGTTGTATTCTGCTTGGTGGATATCTACATCATGCTTGGGAAGGCATTCGTCCCGTATTTGGAAGGGCTTAACAGCACGCAGCTGCGCCTTGTAACTA




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