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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTGATTGTCGGAGGTGGCTACATAGGACTTGAGCTTAGCGCAGCCTTGAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctccttattctttgcatccagaaagatttactactataaattgtgttttctgaatactcaacagcaaggaaacaaatacctctcatctttatagttgtaacgtatttggccaatgaaatctcatattggagatgccatctgttgtag

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G134708_T01 (Zea mays), 5'ss of exon 6
GCTGTGATTGTCGGAGGTGGCTACATAGGACTTGAGCTTAGCGCAGCCTTGAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctccttattctttgcatccagaaagatttactactataaattgtgttttctgaatactcaacagcaaggaaacaaatacctctcatctttatagttgtaacgtatttggccaatgaaatctcatattggagatgccatctgttgtag
||||||||||| |||||||| |||||||| |||||||||||||| |||||||| | |||||| || ||||| || ||||||||||||||||| |||||||||||||||| |||  ||           ||   |||  ||   |  ||   |  |||| |      |       || |||| |||    | | | | ||   ||   | |||||  |  |   |  ||                         
GCTGTGATTGTTGGAGGTGGTTACATAGGGCTTGAGCTTAGCGCTGCCTTGAAAATCAACAACTTCGATGTGACCATGGTGTACCCTGAACCGTGGTGCAgtaagtctcgttaacct----------gaaagcttatcac-gcatgttccatcctctgga------attattctgagacaactactgaccttttctcta--cgttctgaatttgatctcttctacttctag----------------------

upper sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTGTGATTGTCGGAGGTGGCTACATAGGACTTGAGCTTAGCGCAGCCTTGAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcct--tattcttt-gcatccagaaagatttactactataaattgtgttttctgaatactcaacagcaaggaaacaaatacctctcatctttatagttgtaacgtatttggccaatgaaatctcatattggagatgccatctgttgtag
|||||  |||| || || || ||||| || ||||||||||| ||||  || | || ||||||||| |||||||||||||| | |||||||||||||||||||||||   ||  ||| |||| ||          || ||  ||  |   ||     |  |||| ||  ||     | | |                                                                            
GCTGTAGTTGTTGGCGGAGGTTACATTGGTCTTGAGCTTAGTGCAGTTTTAAGGATCAACAATTTAGATGTCACTATGGTTTTCCCTGAACCTTGGTGCAgtaagttgactagtatccttttgctattcatgtaatatatgacatt--gttacacgtaatgaaaacaaaatgttgacgcag---------------------------------------------------------------------------
















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|38568445|gb|CD670660.1|CD670660
EST:     GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
EST: gi|33681535|gb|CF309774.1|CF309774
EST:     AACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: AACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
EST: gi|29636698|gb|CB641707.1|CB641707
EST:     GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
EST: gi|117233824|gb|CT847763.1|CT847763
EST:     GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
EST: gi|58587930|gb|CF986238.1|CF986238
EST:     GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
EST: gi|66912833|gb|CX099681.1|CX099681
EST:     GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
EST: gi|12404688|gb|AU166289.1|AU166289
EST:     GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCA                         TGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG
genomic: GAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACG

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), 75 (downstream exon)
Score: 110

GCTGTGATTGTCGGAGGTGGCTACATAGGACTTGAGCTTAGCGCAGCCTTGAAGACCAACAATTTTGATGTCACTATGGTGTACCCTGAACCTTGGTGCAgtaagtctcc ... tctgttgtagTGCCCCGTCTCTTCACTTCTGGCCTTGCTGCTTTCTACGAGGGATACTACGCTAACAAAGGAATCCATATCATAAAGGGAACCGTGGCTGTTGGTTTTGA




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