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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGTCGGCGCGCCCGCGGCGAGCGTCTTCCGTCTCCCTCTCCACCGCGCCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGGgtacgtgattctgcactcggttggctccacggggtgttgttcttcgtggctgcggttgacgtgatgttttgtggtctcccccattgtgtttgtgccaatg...

Basic information

species Oryza sativa
transcript LOC_Os01g73450.1
intron # 1
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|29686224|gb|CB682499.1|CB682499
EST:     CCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGG                         AGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC
genomic: CCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGGgtacgtgatt ... tatttgacagAGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC
EST: gi|88398746|gb|CI598711.1|CI598711
EST:     CTAGGCCGAGGGCACGCGCCGCCGGCCCCGACTCTCCCTCCAACTTTTGG                         AGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCT
genomic: CTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAAC-TTTGGgtacgtgatt ... tatttgacagAGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCT
EST: gi|88417031|gb|CI573746.1|CI573746
EST:     CCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGG                         AGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGGTC
genomic: CCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGGgtacgtgatt ... tatttgacagAGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC
EST: gi|58585704|gb|CF984012.1|CF984012
EST:     CTATGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCGCCTCCAACTTTGG                         AGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC
genomic: CTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTC-CCTCCAACTTTGGgtacgtgatt ... tatttgacagAGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC
EST: gi|29641572|gb|CB646579.1|CB646579
EST:     CCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGG                         AGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC
genomic: CCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGGgtacgtgatt ... tatttgacagAGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTC

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: 73 (upstream exon), 63 (downstream exon)
Score: 11

CTTCGTCGGCGCGCCCGCGGCGAGCGTCTTCCGTCTCCCTCTCCACCGCGCCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGGgtacgtgatt ... tatttgacagAGGTCAAACATCACTGATGCCACCATTCAGCCTTATGCTTGATGAAGGCTCTAGATCTAAAAAGCCATATAGATGGCAAAGGGTGTTGCTTAAAGTAAGT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGTCGGCGCGCCCGCGGCGAGCGTCTTCCGTCTCCCTCTCCACCGCGCCTAGGCCGAGGGCACGCGCCGCCGGCTCCGACTCTCCCTCCAACTTTGGgtacgtgattctgcactcggttggctccacggggtgttgttcttcgtggctgcggttgacgtgatgttttgtggtctcccccattgtgtttgtgccaatg

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