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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttctgtatgatttatgttgtcttatgtgtttaaaatggttggtgaatgtaaatgtacagaaatgaagttcattttctgtatgtttaccttcagtttcccaaagtagtccaaaaatgtttgggtatcatttctgagcacaatatgttctgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTTCGACC

Basic information

species Oryza sativa
transcript LOC_Os08g34750.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34750.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G820727_T07 (Zea mays), 3'ss of exon 5
gttattttctgtatgatttatgttgtcttatgtgtttaaaatggttggtgaa-tgtaaatgtacagaaatgaagttcattttctgtatgtttaccttcagtttcccaaagtagtccaaaaatgtttgggtatcatttctgagcacaatatgttctgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTTCGACC--------------------------------------------
|||||||  ||||   ||       || | | | ||| ||||| ||| | || |||   |||| |||||| | || | |||  | | ||||||   |                               || |||  ||| || ||| ||| || | ||||||||||| |||||||| ||||||||||| || || |||||||||||||| || || ||||                                            
gttatttagtgtacacttc------tcctttctatttgaaatgattgataaaatgtgtctgtatagaaatcaggtccttttattctttgtttaggct-------------------------------gtgtcaagtctaagtacagtatattattttatgcagATCGGCGTTGCGTTCTTTCAAACGGCGCGTAGCATATGCTAATGCTAATTTTGACCGTATCCTTTAACAGCTTCATCCTTGTCTGTGTACTAATTATTAA

upper sequence: LOC_Os08g34750.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G820727_T05 (Zea mays), 3'ss of exon 5
gttattttctgtatgatttatgttgtcttatgtgtttaaaatggttggtgaa-tgtaaatgtacagaaatgaagttcattttctgtatgtttaccttcagtttcccaaagtagtccaaaaatgtttgggtatcatttctgagcacaatatgttctgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTTCGACC
|||||||  ||||   ||       || | | | ||| ||||| ||| | || |||   |||| |||||| | || | |||  | | ||||||   |                               || |||  ||| || ||| ||| || | ||||||||||| |||||||| ||||||||||| || || |||||||||||||| || || ||||
gttatttagtgtacacttc------tcctttctatttgaaatgattgataaaatgtgtctgtatagaaatcaggtccttttattctttgtttaggct-------------------------------gtgtcaagtctaagtacagtatattattttatgcagATCGGCGTTGCGTTCTTTCAAACGGCGCGTAGCATATGCTAATGCTAATTTTGACC
















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|29687209|gb|CB683484.1|CB683484
EST:     CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
EST: gi|29624696|gb|CB629707.1|CB629707
EST:     CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
EST: gi|27577773|gb|CB000468.1|CB000468
EST:     CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
EST: gi|29677871|gb|CB674146.1|CB674146
EST:     CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
EST: gi|29678642|gb|CB674917.1|CB674917
EST:     CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
EST: gi|27576057|gb|CA998751.1|CA998751
EST:     CGCCCACTCCTTCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
EST: gi|29674047|gb|CB670322.1|CB670322
EST:     CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAG                         ATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT
genomic: CGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTT

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: 64 (upstream exon), 74 (downstream exon)
Score: 12

TTGGGAGAACAGGAAAGCATTTATTCCTTACAGACAATGATGATGGCAGACGCCCACTCCTCCTTCAAATGGTTGATGACTGTGATGATATAAAATTCAGgttattttct ... tgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTTCGACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtccaaaaatgtttgggtatcatttctgagcacaatatgttctgttatgcagATCAGCGTTGCGCTCTTTCAAACGACGTGTGGCATATGCTAATGCAAACTTCGACC
                                          ttctgtt  CT-rich tract
       aaaaatgttt  TA-rich tract