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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAAGATTCCCAGCAAGCTGTCCTCTGTGTTCTGTGGAACCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatctccttttccgacgatcatgcatctcagtttactgtattcttgtctgctgacaaaagcaaccgaaacttacgtatcagtaaagtaggatggt...

Basic information

species Oryza sativa
transcript LOC_Os10g35930.1
intron # 4
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|88402615|gb|CI598842.1|CI598842
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|66947286|gb|AU312130.1|AU312130
EST:     CCAGGACAAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCAGGAC-AAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|87010067|gb|CI279164.1|CI279164
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|11564744|gb|AU165380.1|AU165380
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86437956|gb|CI119876.1|CI119876
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86530068|gb|CI170274.1|CI170274
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|87007075|gb|CI277150.1|CI277150
EST:     CTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|32948518|gb|BP185090.1|BP185090
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86479286|gb|CI121919.1|CI121919
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|87021526|gb|CI274133.1|CI274133
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86846481|gb|CI280818.1|CI280818
EST:     AAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: AAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86480860|gb|CI123493.1|CI123493
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|87027746|gb|CI274310.1|CI274310
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86481089|gb|CI123722.1|CI123722
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|86858554|gb|CI273110.1|CI273110
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
EST: gi|87020814|gb|CI269531.1|CI269531
EST:     CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAG                         ATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT
genomic: CCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCAT

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: 75 (upstream exon), 74 (downstream exon)
Score: 183

GCTAAGATTCCCAGCAAGCTGTCCTCTGTGTTCTGTGGAACCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatct ... ccctatgcagATGACCATGGAGGGTGAGTGTTACCACAGGACCTGCTTCAAGTGCGCCCATGGCGGCTGCCTTCTGACGAACGCCTCCTACGCCTCGCACAACGGGATCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAAGATTCCCAGCAAGCTGTCCTCTGTGTTCTGTGGAACCCAGGACAAGTGTACTGCCTGCAAGAAGACTGTGTATCCATTGGAGAAGgtaataatctccttttccgacgatcatgcatctcagtttactgtattcttgtctgctgacaaaagcaaccgaaacttacgtatcagtaaagtaggatggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA