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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCAGATTTCGGACTTGCAAAATTGACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttctatctacttgtgtagcaagcatcagttcatattttcgaaaaaaaggattaatcaaaatctataataaagaatcattttttaagctagtgcattacagcatcagccgtatcaaaatcagttcccttgtaatacttttcctgcccttag

Basic information

species Oryza sativa
transcript LOC_Os01g12720.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12720.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G170035_T01 (Zea mays), 5'ss of exon 5
GTGGCAGATTTCGGACTTGCAAAATTGACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttctatctacttgtgtagcaa-gcatcagttcatattttcgaaaaaaaggattaatcaaaatctataataaagaatcattttttaagctagtgcat-tacagcatcagccgtatcaaaatcagttcccttgtaatacttttcctgcccttag
||||||||||| |||||||||||||| |||||||||   ||||| || |||||||||||||| ||||||||||||||||| ||||  |||    |||||  |     |||  ||||  |||| |||| |          || | | ||     ||  | || | |  |   | |  |  |||||  |   ||||| ||||     | |  |  |||  || || || | | |||
GTGGCAGATTTTGGACTTGCAAAATTCACTTCTGATGCAAACACCCACGTTTCAACCAGAGTGATGGGCACATTTGGgtacgttcagtcttacggtgtaatattatctcatctcattgtttcaaaaacag---------aagacccatc----agtgttatctgtgtacacaatagacatacagggtataccgtaacaaat----tgctgtgttaaatctcttactcctcatag
















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|38478773|gb|CF962906.1|CF962906
EST:     CTCATGTTTCAACCAGAGTAATGGGCACATTTGG                         GTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCGAGCTGAGAAATCAGA
genomic: CTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttcta ... ctgcccttagGTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA
EST: gi|40491605|gb|BX901601.1|BX901601
EST:     ACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGG                         GTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA
genomic: ACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttcta ... ctgcccttagGTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA
EST: gi|58590206|gb|CF988514.1|CF988514
EST:     ACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGG                         GTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA
genomic: ACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttcta ... ctgcccttagGTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA
EST: gi|66912790|gb|CX099638.1|CX099638
EST:     ACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGG                         GTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA
genomic: ACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttcta ... ctgcccttagGTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGA

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: 75 (upstream exon), 74 (downstream exon)
Score: 33

GTGGCAGATTTCGGACTTGCAAAATTGACTTCTGATAATAACACTCATGTTTCAACCAGAGTAATGGGCACATTTGGgtatgttcta ... ctgcccttagGTACCTTGCACCAGAGTATGCGTCTTCTGGCCAGCTAACTGAGAAATCAGATGTCTTTTCTTTCGGAGTAATGCTTCTTGAGCTAATAACTGGCCGCCGT




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