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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTACTCCCAAGGGTGTGTTAAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagttgtccctattgcatgatatttttgtgaaaaaaaattattcttatcttttcattttgagttaatttattttgcag

Basic information

species Oryza sativa
transcript LOC_Os07g25710.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g25710.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G162409_T01 (Zea mays), 5'ss of exon 4
AAGCTACTCCCAAGGGTGTGTTAAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagttgtccctattgcatgatatttttgtgaaaa----aaaattattcttatcttttcattttgagttaatttattttgcag
|||| ||||| ||||||||  | |||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||  |  ||||||||   ||  || |||  || |    |||||||||||  | | |  |||||   | |   | | || |||
AAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTAAAAAGTCATCTTCAGgtctgatatctagccctattgttggacgttattgaaaatagctgaaaattattctc-tatctgaattttatctaacaatgtgtttcag

upper sequence: LOC_Os07g25710.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G162409_T05 (Zea mays), 5'ss of exon 3
-----------------------AAGCTACTCCCAAGGGTGTGTTAAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagttgtccctattgcatgatatttttgtgaaaa----aaaattattcttatcttttcattttgagttaatttattttgcag
                       |||| ||||| ||||||||  | |||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||  |  ||||||||   ||  || |||  || |    |||||||||||  | | |  |||||   | |   | | || |||
ACATTTTCCTTAAATTGTTGCAGAAGCAACTCCTAAGGGTGTCCTGAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTAAAAAGTCATCTTCAGgtctgatatctagccctattgttggacgttattgaaaatagctgaaaattattctc-tatctgaattttatctaacaatgtgtttcag
















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|29673026|gb|CB669301.1|CB669301
EST:     GACCATTTATCATGTTAAAAGTCACCTTCAG                         AAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG
genomic: GACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagt ... tattttgcagAAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG
EST: gi|88272430|gb|CI386285.1|CI386285
EST:     TAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAG                         AAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG
genomic: TAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagt ... tattttgcagAAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG
EST: gi|58685772|gb|CK074459.1|CK074459
EST:     TAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAG                         AAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG
genomic: TAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagt ... tattttgcagAAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG
EST: gi|58669237|gb|CK057923.1|CK057923
EST:     TAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAG                         AAATACAGAACAGCTCG
genomic: TAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagt ... tattttgcagAAATACAGAACAGCTCG

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), 40 (downstream exon)
Score: 26

AAGCTACTCCCAAGGGTGTGTTAAAGCTAATGAAGGCAGACAATTTGACCATTTATCATGTTAAAAGTCACCTTCAGgtctgttagt ... tattttgcagAAATACAGAACAGCTCGATACAGACCAGAATTGTCTGAAG




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