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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaactatatggccaatgatatttccttttttttgttaattactctttgttcccttacctatcgacctcagtaatctgtaggagatccatacct...

Basic information

species Oryza sativa
transcript LOC_Os04g59494.4
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 20
TGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaactatatggccaatgatatttccttttttttgttaattactctttgttcccttacctatcgacctcagta-atctgtaggagatccatacct
| |||||||||||||  | |||||||  ||||||||||| ||| | ||||| ||  |||| |||||||||||||| |||||||||||||||||||| || |||| |||     | | ||  ||| ||||   ||   |||       ||        | || || || | || |  ||   || |  |  ||   | |   
TACTGCAGCTGGTGCGGTGTATGATAGAGAATTCATTGTTTGTTCGTTGGACCTACTGTCTGGACTTGCAGAAGGTCTTGGCGCTGGTATTGAAAGTCTTgtaagttcttgcct-ttgcatatggtattgttttccctttcaagtacacaaacacaccactcacatacccacatgggtgcgtccggggtggagttagatta
















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|58608072|gb|CK036105.1|CK036105
EST:     ATCTG-TGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTGGGGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58671684|gb|CK060370.1|CK060370
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|29623086|gb|CB628097.1|CB628097
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58611878|gb|CK039590.1|CK039590
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58667508|gb|CK056194.1|CK056194
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58592654|gb|CF990962.1|CF990962
EST:     TCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCGGG                         GGTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGA
genomic: TCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCC-TGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGA

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: 56 (upstream exon), 71 (downstream exon)
Score: 33

TGCTGCAGCTGGTGCATTATATGATAAGGAATTCATTGTGTGTGCATTGGATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAAGCAGCGGATGTTCGACAGAGTGCTCTCGCCCTCCTGGGGGACCTTTCTA




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