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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttgatgtcatgcttgaagtggtccagagcaggcacattattttccctgttacactttaaaaaaaaacccaagaaacattgatttcctcctccatataactgtaaaaggcttattctactcaaaatatccaagcatctagttaattattgttattctgctttgcagGTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGGTAAGTCTCTGCCTTAA

Basic information

species Oryza sativa
transcript LOC_Os01g51200.2
intron # 10
splice site 3'
intron type U2

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|163926649|gb|EG713665.1|EG713665
EST:     TGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAG                         GTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAAT
genomic: TGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAGgttagttttg ... tgctttgcagGTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAAT
EST: gi|58681515|gb|CK070202.1|CK070202
EST:     TGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAG                         GTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAAT
genomic: TGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAGgttagttttg ... tgctttgcagGTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAAT
EST: gi|58586454|gb|CF984762.1|CF984762
EST:     TGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAG                         GTTTTCCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAA
genomic: TGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAGgttagttttg ... tgctttgcagGTTTTC-AGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAA

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: 63 (upstream exon), 74 (downstream exon)
Score: 46

TTTGCATCATATTTCCACTATTGCCGCTCACTGCGGTTTGATGACAAGCCTGATTATTCCTACCTTAAGCGACTTTTCCGTGACCTTTTTATCCGGGAAGgttagttttg ... tgctttgcagGTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGGTAAGTCTCTGCCTTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctactcaaaatatccaagcatctagttaattattgttattctgctttgcagGTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGGTAAGTCTCTGCCTTAA
                           agttaat  putative branch site (score: 46)
                                          ttctgcttt  putative PPT
                       atctagttaattattg  TA-rich tract