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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatcagatttttttgttgttttgtacaggaaagtcgaagcactttgtacttgatcttaccttttgtgaagttctttttttcatcttcttgctatccaatggtacagcctatacagtgtaccatgtgctaacactagacatggttcttgtttactgacaagcttatctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT

Basic information

species Oryza sativa
transcript LOC_Os01g56630.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 10
gtacgtatcagatttttttgttgttttgtacaggaaagtcgaagcactttgtacttgatcttaccttttgtgaagttctttttttcatcttcttgctatccaatggtacagcctatacagtgtaccatgtgctaacactagacatggttcttgtttactgacaagcttatctac---tatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT
||| |||||||| | ||| |||||| ||||||||||||| |||  |||  ||  ||| ||| |||  ||| ||||||   ||||  |  | | | ||||    || |||||  | ||   ||   | ||    |  | | |   |  |   |||||| ||| |||||| | |||   |  |||||||||||||||| |||||||| ||||| ||| ||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||| ||||| ||||
gtaggtatcagaatcttt-gttgttctgtacaggaaagttgaa--actaggtctttggtct-accaattg-gaagtttccttttgaacttccctactatttgctgctacagtttttattttg---cgtgcaacactatttgtagtactaactgtttaatgataagcttgtatacacttgcagGATGTCTACCTTCACACAAACTGTCTTGCTATTTTAGCAAACATGGCTCCTCATGTGCATAGGCTGAGTGCTTATGCATCACAAAGGCTAGTTAGTCTCT

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G078576_T03 (Zea mays), 3'ss of exon 9
gtacgtatcagatttttttgttgttttgtacaggaaagtcgaagcactttgtacttgatcttaccttttgtgaagttctttttttcatcttcttgctatccaatggtacagcctatacagtgtaccatgtgctaacactagacatggttcttgtttactgacaagcttatctac---tatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT
||| |||||||| | ||  |||||||||||||| ||| | |||  |||  || | |||||  |||  ||| |||  |   ||||  |  ||  ||||||  | || || ||  | ||| |||| | |  |      | | |   || |   |||||| ||| ||| |||| |||   |  |||||||||||||||| |||||||| ||||||||| ||||||||||||| || |||||||||||||||||||| |||||||| |||||||| ||||| ||||
gtaggtatcagaatcttc-gttgttttgtacag-aaaatagaa--actaggttcctgatc--accaattg-gaaactgccttttgaactttgctgctatttactgctatagtttgtactgtgtgcaacat-----tatttgtagtgctaactgtttaatgataagattatatacacttgcagGATGTCTACCTTCACACAAACTGTCTTGCAATTTTAGCAAATATGGCTCCGCATGTGCATAGGCTGAGTGCTTATGCATCACAAAGGCTAGTTAGTCTCT
















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|58684083|gb|CK072770.1|CK072770
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|29628456|gb|CB633467.1|CB633467
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|58693104|gb|CK081791.1|CK081791
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGA                         GATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT
genomic: TGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCT

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: 66 (upstream exon), 72 (downstream exon)
Score: 19

CCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCTTTGGGATCTTTGATGGTTGTTATACTAATCCGAACCATCAAATACAACCTCTCCAAACTGCGAgtacgtatca ... tctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgtgctaacactagacatggttcttgtttactgacaagcttatctactatagGATGTCTACCTTCATACAAACTGCCTTGCAATTCTAGCAAATATGGCCCCTCATGTGCATAGGCTGAGTGCATATGCATCTCAAAGGCTGGTTAGCCTCT
                               tactgac  putative branch site (score: 19)
                                         cttatct  putative PPT
                          ttgttta  TA-rich tract