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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacatatgatcttctcttgttcattattgtgctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtag

Basic information

species Oryza sativa
transcript LOC_Os05g07130.1
intron # 22
splice site 5'
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|58611022|gb|CK038734.1|CK038734
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86850852|gb|CI338828.1|CI338828
EST:     TATATGCATATTTCGCTTACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29629510|gb|CB634519.1|CB634519
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACCCCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29616012|gb|CB621024.1|CB621024
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|16578926|gb|BI813021.1|BI813021
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACCAAATGGGAGTCACAGGTGTTGA
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATAC-AAATGGGAGTCACAGGTGTTGA
EST: gi|86842389|gb|CI335281.1|CI335281
EST:     ATATGCATATTTCGCTGACAGGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTTTTGAG
genomic: ATATGCATATTTCGCTGACA-GGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86838836|gb|CI330278.1|CI330278
EST:     TATATGCATATTTCCCTGACAGGCCTCTGA-GGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29612782|gb|CB617795.1|CB617795
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29615977|gb|CB620989.1|CB620989
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86868850|gb|CI334222.1|CI334222
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86853669|gb|CI330520.1|CI330520
EST:     TATATGCATATTTCGCTGACAGCCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|88844562|gb|CI020409.1|CI020409
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29615975|gb|CB620987.1|CB620987
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29616052|gb|CB621064.1|CB621064
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86869030|gb|CI335597.1|CI335597
EST:     TATATCCATATTTCGCTCACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG

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), 70 (downstream exon)
Score: 38

GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG




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