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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCAGGTGATTCTCTAGATCATTGTGATAAGCTCATTGAGTTGGTTGCTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgttatattctttttatttggtcaatataaattacttgtgaacttcttaatgtcaacagcaatattttgtaattaattcag

Basic information

species Oryza sativa
transcript LOC_Os11g42420.2
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42420.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G348675_T02 (Zea mays), 5'ss of exon 23
TGAAGCAGGTGATTCTCTAGATCATTGTGATAAGCTCATTGAGTTGGTTGCTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgttatattctttttatttg---gtcaatataaattact--tgtgaacttcttaatgtcaacagcaatattttgtaattaatt--cag
|||   || | | ||||||||| | |||||  | ||  ||||||| |||| |||| | || |||||||| ||||||||||||||||| |||||||||||||| | |  ||    | |||  ||||    || |          |  | ||  |  | | | | |||||  | | || |  ||||  ||  |||
TGATCTAGATTACTCTCTAGATAAATGTGACGAACTTGTTGAGTTAGTTGGTTCAGCCGAGTCTGGAATGATGCATTTGTTCAGCCAGCAGCAGTTGCAGgtcacttctaatgacctttcgtttgttaatccactcgggcccttattctgcccaccctgacgccaacaaaattgttgttcaattgtttgtcag
















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|86535775|gb|CI175981.1|CI175981
EST:     CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAG                         GAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
genomic: CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgtta ... attaattcagGAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
EST: gi|29669547|gb|CB665822.1|CB665822
EST:     CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAG                         GAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
genomic: CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgtta ... attaattcagGAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
EST: gi|58665324|gb|CK054010.1|CK054010
EST:     TTCCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAG                         GAATTCCTGCTTTT
genomic: TTC-ATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgtta ... attaattcagGAATTCCTGCTTTT
EST: gi|86481393|gb|CI124026.1|CI124026
EST:     CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAG                         GAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
genomic: CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgtta ... attaattcagGAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
EST: gi|218482307|gb|FG954939.1|FG954939
EST:     CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAG                         GAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG
genomic: CTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgtta ... attaattcagGAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAG

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: 58 (upstream exon), 56 (downstream exon)
Score: 15

TGAAGCAGGTGATTCTCTAGATCATTGTGATAAGCTCATTGAGTTGGTTGCTTCATCGGAATCTGGAATAATGCATTTGTTCAGCCAACAGCAGTTGCAGgttagtgtta ... attaattcagGAATTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAGGAAGAGCAGTTAGAGCAGTTACCTGCTGATGGCTAAAAGGTTGATGTTA




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