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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgacctgcaaagtaccactgatacttaaattgacctaaatctgaactggtaagtttaaaatgatgctgttgtcttatttttacctcttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTGTACAATATTTGCACCACTCAGTTTAGCCGATCGGTAAATTTCCTTAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g67920.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67920.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G025451_T01 (Zea mays), 3'ss of exon 10
gtgatgacctgcaaagtaccactgatacttaaattga----cctaaatctgaactggtaagtttaaaatgatgctgttg--------------------tcttatttttacctcttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTGTACAATATTTGCACCACTCAGTTTAGCCGATCGGTAAATTTCCTTAAAG
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gtgatgctttgcaaactgttagcagaaactaaatttattctcttcaatctga-ttggcaagtgcaaaacctggacatgggaaagtaacaaaataaacattcttatgtttgaaattctgttacagGCAATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGCCTGTACAATATTTGCATGACCCGGTTCAGCAGGTCTGTAAATTTTCTTAAAG
















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|33682408|gb|CF310647.1|CF310647
EST:     AAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAG                         GCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
genomic: AAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAGgtgatgacct ... ttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
EST: gi|58612799|gb|CK040511.1|CK040511
EST:     ATTAATCTTGAGTGATGTAGGGAGAGCGAGCTCTTTATACACTAAAACAG                         GCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
genomic: ATTAATC-TGAGTGATGTA-GAAGAGCGAGCTCTTTATACACTAAAACAGgtgatgacct ... ttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
EST: gi|29641528|gb|CB646535.1|CB646535
EST:     AAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAG                         GCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
genomic: AAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAGgtgatgacct ... ttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
EST: gi|58663420|gb|CK052106.1|CK052106
EST:     AAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAG                         GCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG
genomic: AAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAGgtgatgacct ... ttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTG

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: 41 (upstream exon), 65 (downstream exon)
Score: 9

AATGGCTCATAGGGCACAGCATGAAATCGCTGCTGCTTATGATACTGAACAAATTAATCTGAGTGATGTAGAAGAGCGAGCTCTTTATACACTAAAACAGgtgatgacct ... ttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTGTACAATATTTGCACCACTCAGTTTAGCCGATCGGTAAATTTCCTTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaactggtaagtttaaaatgatgctgttgtcttatttttacctcttatttgcagGCTATCCAAGAGGACCCAGATGATGCTGTTCAATGGCATCAACTTGGTTTGTACAATATTTGCACCACTCAGTTTAGCCGATCGGTAAATTTCCTTAAAG
                              tcttatttttacctct  CT-rich tract
 taagtttaaaatgat  TA-rich tract