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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCAGGGAAGAATTCAAGAGTTGTACAATGCTTATAATTGCTCACCGCCTGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgcttttgaagagatgtttcttcttttgttctggtgctttgcctctcatttgaatagtacaacaataaattcctgataatatcaacatgcttgatag...

Basic information

species Oryza sativa
transcript LOC_Os04g52900.2
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G084181_T01 (Zea mays), 5'ss of exon 25
AATCAGGGAAGAATTCAAGAGTTGTACAATGCTTATAATTGCTCACCGCCTGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgcttttgaagagatgtttcttcttttgttctggtgctttgcctctcatttgaatagtacaacaataaattcctgataatatcaacatgcttgatag-------
|||| | ||||||||||||||||| |||||||| |||||||| |||||  ||||||| || |||||||||||||||||||||||||||||| ||||| ||||||| || |       | | |||| ||||||| ||     |||  ||| ||   |   |||    |  |  ||| || | || |    ||  ||| |||       
AATCCGAGAAGAATTCAAGAGTTGCACAATGCTCATAATTGCCCACCGTTTGAACACGGTCATTGACTGTGACAGGTTGCTTATTCTAAGTTCTGGGCAGgtatg-ttctatccttttatgtcttgttttgttgtg----cttgattcttataatagctgtatgttagcattttcatg-tcatgtgctgattattg-tagtgttact
















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|33685919|gb|CF314158.1|CF314158
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|112787004|gb|EE591866.1|EE591866
EST:     GACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: GACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|88354423|gb|CI624813.1|CI624813
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|38481628|gb|CF965717.1|CF965717
EST:     TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAG                         GTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: TGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
EST: gi|38477879|gb|CF962012.1|CF962012
EST:     CTAAGTGCTGGG-AG                         G-TTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT
genomic: CTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCT

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: 72 (upstream exon), 40 (downstream exon)
Score: 19

AATCAGGGAAGAATTCAAGAGTTGTACAATGCTTATAATTGCTCACCGCCTGAACACTGTTATTGACTGTGACAGGTTGCTTATTCTAAGTGCTGGGAAGgtatgctttt ... tacttttcagGTTTTGGAGTTCGACTCTCCTGAGAATCTTTTGAGCAATGAGCACAGTGCTTTCTCCAAGATGGTTCAGAGTACAGGACCTAGCAATGCAGAGTACCTGA




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