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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGATTTAGTTCTGAATTGATGCCAAAGGGACATGAGAAGGAAAGCCAAGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgtggttgatgatttccccctgtatacttatttattatgctgatgtcaaaattttatctcag

Basic information

species Oryza sativa
transcript LOC_Os01g56600.1
intron # 8
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|86426337|gb|CI071434.1|CI071434
EST:     CCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: CCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|25800862|gb|CA756823.1|CA756823
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|58677969|gb|CK066656.1|CK066656
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|58652432|gb|CK041112.1|CK041112
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|218494657|gb|FG954317.1|FG954317
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|88243199|gb|CI244321.1|CI244321
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|86427812|gb|CI072909.1|CI072909
EST:     AAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|58690175|gb|CK078862.1|CK078862
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|3763619|gb|AU030371.1|AU030371
EST:     AGCTAAGATTAA-CGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGANAGCACAA-TCCCTAAATTGATGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCC-TAAATTGATGA
EST: gi|86885189|gb|CI316949.1|CI316949
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTC-G
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagA-GCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGG
EST: gi|25807131|gb|CA763092.1|CA763092
EST:     AAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|88215986|gb|CI215835.1|CI215835
EST:     TAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: TAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|86427977|gb|CI073074.1|CI073074
EST:     GATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: GATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|86499773|gb|CI142406.1|CI142406
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|88831470|gb|CI083864.1|CI083864
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
EST: gi|86494313|gb|CI136946.1|CI136946
EST:     AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAG                         AGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA
genomic: AGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGA

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), 73 (downstream exon)
Score: 50

CCTGGATTTAGTTCTGAATTGATGCCAAAGGGACATGAGAAGGAAAGCCAAGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgt ... tttatctcagAGCTTGACAGCACAAATCCTAAATTGATGACTGAATCGCGTATTCTTCGGATTGCTCGGGGATCTGGCCGACCTGTCAGAGATGTTGTCGACATGCTCGA




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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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGATTTAGTTCTGAATTGATGCCAAAGGGACATGAGAAGGAAAGCCAAGCTAAGATTAAACGGTACATGACGATGATGGATTCCATGACAGATGGAGgtgagtgtgtggttgatgatttccccctgtatacttatttattatgctgatgtcaaaattttatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA