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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgagagggctctctggccttgcaccccaggtgtttgtggttttgccttacaggggagtggttttgagttttgttctgtgggttggcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCGCACATTCTTGTGTTCAGTGAGGACCTCTTCTTCATTTATTTGCTTCCAC

Basic information

species Oryza sativa
transcript LOC_Os05g05590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 2
gtgaga-tgagagggctctctggccttgcaccccaggtgtttgtggttttgccttacaggggagtggttttgagttttgttctgtgggttggcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCGCACATTCTTGTGTTCAGTGAGGACCTCTTCTTCATTTATTTGCTTCCAC
||| |  |    || |||      || |||  || ||||| ||||||||||| ||    |||    | ||||||| || || |     ||   |  || |||| || ||||| ||||| || || ||||| || | |  |||||  ||||| | ||||||||||||||| |||||||| || ||||| ||||| ||||| |
gtggggctctccggcctccgctctctcgcagtccgggtgtctgtggttttgc-ttctgtgggcactgctttgagtgttcttgt-----ttcctgtatgtagGGCCTCATCACCGGAGGCGTCATCCTGCTGGTTACTAATGGGACAAACTCACGCATTCTTGTGTTCAGCGAGGACCTGTTTTTCATATATTTACTTCCGC
















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|29677872|gb|CB674147.1|CB674147
EST:     TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATG                         GGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
genomic: TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
EST: gi|29628630|gb|CB633641.1|CB633641
EST:     TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATG                         GGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
genomic: TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
EST: gi|58663671|gb|CK052357.1|CK052357
EST:     TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATG                         GGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
genomic: TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
EST: gi|88501783|gb|CI695221.1|CI695221
EST:     TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATG                         GGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
genomic: TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
EST: gi|88427391|gb|CI569429.1|CI569429
EST:     TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATG                         GGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
genomic: TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
EST: gi|29633364|gb|CB638373.1|CB638373
EST:     TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATG                         GGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG
genomic: TGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCG

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: 71 (upstream exon), 63 (downstream exon)
Score: 27

GATCAACATCTTCGTGGCGCTGCTGTGCAGCTGCATTGTGATCGGGCACCTGCTGGAAGGGAACCGGTGGGTCAATGAATCCATCACCGCGCTTGTCATGgtgagatgag ... gcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCGCACATTCTTGTGTTCAGTGAGGACCTCTTCTTCATTTATTTGCTTCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgccttacaggggagtggttttgagttttgttctgtgggttggcgcttgcagGGGCTGATCACTGGAGGTGTGATTCTGCTCGTCAGTGGTGGGAAGAACTCGCACATTCTTGTGTTCAGTGAGGACCTCTTCTTCATTTATTTGCTTCCAC
    gccttac  putative branch site (score: 27)
                            ttttgtt  TA-rich tract