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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttctattgtggtccagaaatagatttatgcatatcagatgatttttctatatatgtgctttgtcattggaacag

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g09000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G158489_T02 (Zea mays), 5'ss of exon 4
GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttctattgtggtccagaaatagatttatgcatat-------cagatgatttttctatatatgtgc-tttgtcattggaacag
||||||||||| || || ||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| | ||||  |||||  |  |||  |  |  |||||  |        |||     ||||   || || |   || |||| |||| |||
GATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAGgtgtgcttttaattgttcttgagagctgtacatatgcggaatttaaggcaggcagattttgattagatttttgttcgtcactggagcag

upper sequence: LOC_Os07g09000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G158489_T03 (Zea mays), 5'ss of exon 4
GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttctattgtggtccagaaatagatttatgcatat-------cagatgatttttctatatatgtgc-tttgtcattggaacag-----------
||||||||||| || || ||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| | ||||  |||||  |  |||  |  |  |||||  |        |||     ||||   || || |   || |||| |||| |||           
GATGAGAAGATCGAGTGCTGCCGCTTTTCTAGGGATGGCATGAAACCGTTCCTGTTTTGCACTGTTGCAAAAGgtgtgcttttaattgttcttgagagctgtacatatgcggaatttaaggcaggcagattttgattagatttttgttcgtcactggagcaggtcccaaagtt
















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|58674632|gb|CK063319.1|CK063319
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|58603054|gb|CK013582.1|CK013582
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|30228290|gb|CB966181.1|CB966181
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCCAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|29640028|gb|CB645037.1|CB645037
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|58687497|gb|CK076184.1|CK076184
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|163918152|gb|EG714798.1|EG714798
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|29627838|gb|CB632849.1|CB632849
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|88395653|gb|CI590668.1|CI590668
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|27410230|gb|CA923300.1|CA923300
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACCGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
EST: gi|29674145|gb|CB670420.1|CB670420
EST:     CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAG                         GTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG
genomic: CTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTG

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: 69 (upstream exon), 70 (downstream exon)
Score: 20

GATGAGAAGATTGAATGTTGCCGCTTTTCTAGGGATGGCATGAAACCATTCCTGTTTTGCACCGTTGCAAAAGgtatactttc ... attggaacagGTAACAAAGTTGTAACTGTTGTCTGGAACATAAGTGACTGGAGTCGAATTGGATACAAGAGACTTCTGGGAAAACCTATCTCCACACTTTCAGTTAGCAT




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