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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaagatgttctccatctaaacttgtagagtacctctggatttgaactgctttgtgcttagtaatctgatcaaattgtgctcgaaattattttag

Basic information

species Oryza sativa
transcript LOC_Os03g11200.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G178294_T04 (Zea mays), 5'ss of exon 13
TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaagatgttctccatctaaacttgtagagtacctctggatttgaactgctttgtgcttagtaatctgatcaaattgtgctcgaaattatt--ttag-----------------------
 |||||||| |||||||||||||||||||||||||||||||| ||  ||||||||||||||||||| || || || ||||||||||||||| | || |||||| ||    |  |  |   | ||| ||  ||| | | |||  |||  |||          | ||  ||||    ||||| || |  ||||   |   |                         
ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtttaattccatcccaaatttacagaatgcttctcaattataac------acattaaggtatcttcctaaattttgttgcaaatgggtgactgacatgtcatgcaatctttcctcag

upper sequence: LOC_Os03g11200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G178294_T01 (Zea mays), 5'ss of exon 12
TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaagatgttctccatctaaacttgtagagtacctctggatttgaactgctttgtgcttagtaatctgatcaaattgtgctcgaaattatt--ttag-----
 |||||||| |||||||||||||||||||||||||||||||| ||  ||||||||||||||||||| || || || ||||||||||||||| | || |||||| ||    |  |  |   | ||| ||  ||| | | |||  |||  |||          | ||  ||||    ||||| || |  ||||   |   |       
ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtttaattccatcccaaatttacagaatgcttctcaattataac------acattaaggtatcttcctaaattttgttgcaaatgggtgactgacatgt

upper sequence: LOC_Os03g11200.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G808775_T01 (Zea mays), 5'ss of exon 7
TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaagatgttctccatctaaacttgtagagtacctctggatttgaactgctttgtgcttagtaatctgatcaaattgtgctcgaaattattttag-------
 |||||||| ||||||||||| |||||||||||||||||||| ||  ||||||||||| ||||||| || ||||| ||||||||||||||| | | ||||||| ||    || | ||   ||||| ||  ||| | | |||  |||  |||          | ||  ||||    ||| | |  |  |||| |     |       
ATATCCTGCATATGGAACTTATGACTACAGCCATCAAATGCCACAGCCTGCTCCTCAAACAGCTGCCTATGGCGCTTATCCTCCAACATACTCTGTTCAGgtattgtgtttgatttctgcctaaatttagagaatgcttctcaattataac------acattgaggcatcttcctaaagtttattgcaaatgaggactgacaactg

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|29629938|gb|CB634947.1|CB634947
EST:     CTCCTCAAGCAGCTGCTTACGGTGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|29628808|gb|CB633819.1|CB633819
EST:     CTCCTCAAGCAGCTGCTTACGGTGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|89174096|gb|CI041989.1|CI041989
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88462893|gb|CI519805.1|CI519805
EST:     CTCAAGCAGGCTGCTTACGGCGCCTATCCTCCNACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCAAGCA-GCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|89184800|gb|CI048356.1|CI048356
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCTACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88471611|gb|CI408882.1|CI408882
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86499191|gb|CI141824.1|CI141824
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|89176256|gb|CI043277.1|CI043277
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86497082|gb|CI139715.1|CI139715
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|58671000|gb|CK059686.1|CK059686
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|87041196|gb|CI195818.1|CI195818
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|24468907|gb|CA305856.1|CA305856
EST:     CTCCTCAAGCAGCTGCTTACGGTGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88850543|gb|CI093224.1|CI093224
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACTTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88487861|gb|CI425132.1|CI425132
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86493516|gb|CI136149.1|CI136149
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88200911|gb|CI198763.1|CI198763
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86479247|gb|CI121880.1|CI121880
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88555936|gb|CI486232.1|CI486232
EST:     TACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: TACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86827107|gb|CI270823.1|CI270823
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|163917703|gb|EG711261.1|EG711261
EST:     CTCCTCAAGCAGCTGCTTACGGTGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|29625008|gb|CB630019.1|CB630019
EST:     CTCCTCAAGCAGCTGCTTACGGTGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88543035|gb|CI470404.1|CI470404
EST:     TCCTCAAGCAGCTGGCTTACGGCGCCTATCCTCCAACATACCCCGTTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCACCAATGGCGGTGGCGGCA
genomic: TCCTCAAGCAGCT-GCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88236165|gb|CI235367.1|CI235367
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|89175874|gb|CI042895.1|CI042895
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|89194661|gb|CI117098.1|CI117098
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88222149|gb|CI222105.1|CI222105
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88849567|gb|CI089475.1|CI089475
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACTAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86480699|gb|CI123332.1|CI123332
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88222399|gb|CI222355.1|CI222355
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACATACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|88508371|gb|CI435877.1|CI435877
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
EST: gi|86482600|gb|CI125233.1|CI125233
EST:     CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAG                         GCCTACACACAACTAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA
genomic: CTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCA

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: 59 (upstream exon), 66 (downstream exon)
Score: 2

TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaaga ... attattttagGCCTACACACAACAAACCTATGCACAACCTTCAGCAATGGCGGTGGCGGCACCAGCACCCGCAGTGGCACCGGCGGCAGCTTACCCTCAGCAACCTGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaagatgttctccatctaaacttgtagagtacctctggatttgaactgctttgtgcttagtaatctgatcaaattgtgctcgaaattattttag

- - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT