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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgcatccttctaaaccttgcaccatttttccttgctattactcatctgactacttaagtataaccgaaagcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCTAGCAAAAAACGCCTAGCCAAGCATGTGTTGGATGTGACAGGTGTTACAA

Basic information

species Oryza sativa
transcript LOC_Os01g63270.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 10
gtatgtgtgcatccttctaaaccttgcaccatttttccttgctattactcatctgactacttaagtataaccgaaagcgtt--acagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCTAGCAAAAAACGCCTAGCCAAGCATGTGTTGGATGTGACAGGTGTTACAA
||||||| ||    | ||||  |||  | | ||  | ||   | | | |  |||  | ||   |||||||| |||| ||||  |||||||||||||||||||||||||||||||||||||||| |||| |||||  || |||| || ||||| ||||| |||||||||||||||||||||||||| |
gtatgtg-gctatatgctaatgcttctaaccttgcttctgcttgtcattactctatccac---agtataactgaaaacgttcaacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCAGCAGCCAAGTTATCTTGCAAGAAGCGCCTGGCCAAACATGTGTTGGATGTGACAGGTGTTACGA
















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|29623807|gb|CB628818.1|CB628818
EST:     AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAACTAAGTTGGCT
genomic: AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgc ... agcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
EST: gi|58610009|gb|CK038042.1|CK038042
EST:     AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
genomic: AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgc ... agcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
EST: gi|699986|gb|D46277.1|D46277
EST:     AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
genomic: AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgc ... agcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
EST: gi|29623647|gb|CB628658.1|CB628658
EST:     AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAA                         TTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
genomic: AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgc ... agcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCT
EST: gi|58657279|gb|CK045959.1|CK045959
EST:     AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAA                         TTTGCAGATGATGAAAAGCTTCATGCT
genomic: AAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgc ... agcgttacagTTTGCAGATGATGAAAAGCTTCATGCT

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), 74 (downstream exon)
Score: 71

GCTCCGTTTCTGCAACCCAGAGTTGAGTGAAATAGTAACAAAATGGCTAAAAACAGATCAGTGGACAAGCAACCTTGATCTTCTTACCGGACTTCGGAAAgtatgtgtgc ... agcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCTAGCAAAAAACGCCTAGCCAAGCATGTGTTGGATGTGACAGGTGTTACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttccttgctattactcatctgactacttaagtataaccgaaagcgttacagTTTGCAGATGATGAAAAGCTTCATGCTGAGTGGGCATCAGCTAAGTTGGCTAGCAAAAAACGCCTAGCCAAGCATGTGTTGGATGTGACAGGTGTTACAA
                                  gtataac  putative branch site (score: 71)
                              ttaagtataa  TA-rich tract