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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGCAACCCGGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaacaacatcttcctcgtcgattgccaagcttgttcgtctccattgatggtgagatataagcgagtgaagtgactgatgtttgcaatggtttgatcag

Basic information

species Oryza sativa
transcript LOC_Os01g04950.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04950.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G020484_T08 (Zea mays), 5'ss of exon 2
GCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGCAACCCGGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaa-caaca-tcttcctcgtcgattgccaagcttgttcgtctccattgatggtgagatataagcgagtgaagtgactgatgtttgcaatggtttgatcag--------
|  || ||||| ||||||||||| || ||||||||| | || || || || |||   ||||||  ||||||||||||||| ||||||||||||||||||||| |||   ||  | || |    ||| ||||||   ||  || ||   |  |  || |    | |   ||| |  | |||| |  | |   | |    || |           
GTTGAGGACATGTACACCCAAGACGGGACCGTGGACATGAAAGGGAATCCCGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctcagtagtcatttgtgtccattgccgctctgctttgtgctcgctc-tgtttgtttgttgtcgactccattgacggccgctgatacttacatggttgatggttcag
















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|58669344|gb|CK058030.1|CK058030
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCCTGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88358200|gb|CI605125.1|CI605125
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88314293|gb|CI602625.1|CI602625
EST:     GGCCACCAAGAACAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88762509|gb|CI772065.1|CI772065
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88414987|gb|CI601819.1|CI601819
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         TTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|29646409|gb|CB651416.1|CB651416
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88745560|gb|CI768920.1|CI768920
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|117229908|gb|CT846338.1|CT846338
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88363891|gb|CI607201.1|CI607201
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88726212|gb|CI749867.1|CI749867
EST:     GGCCACCAACAACAACACCGGCAACTGGCGTGCCTGCCCCTANATCCTCG                         CTAACGAGTGCTGGGAGAGGCTGGC
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGC
EST: gi|88316937|gb|CI625574.1|CI625574
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88395178|gb|CI609494.1|CI609494
EST:     GCCACCAAGAAGAACACCGGCCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGACCACCAACCTCG
genomic: GCCACCAAGAAGAACACCGGC-AACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88402788|gb|CI613236.1|CI613236
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88370557|gb|CI590135.1|CI590135
EST:     GGCCACCAAGAAGAACACCGGCAAGTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88739283|gb|CI762791.1|CI762791
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|58609810|gb|CK037843.1|CK037843
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTA-AGGCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|58664808|gb|CK053494.1|CK053494
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88736884|gb|CI760392.1|CI760392
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88723934|gb|CI745631.1|CI745631
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACC
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACC
EST: gi|88736975|gb|CI760483.1|CI760483
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88763877|gb|CI773293.1|CI773293
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|58673905|gb|CK062591.1|CK062591
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|88400151|gb|CI590841.1|CI590841
EST:     GGGCACCAAGAAGAACACCGGCAACTGGCGTGCCTGGCCCTACATCCTCG                         CTAACGAGTGGTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
EST: gi|58693491|gb|CK082178.1|CK082178
EST:     GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCG                         CTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG
genomic: GGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCG

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: 71 (upstream exon), 72 (downstream exon)
Score: 9

GCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGCAACCCGGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaaca ... gtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCGTGAACTACATGAAGACGCGGCTCGGGCAGGAGAGCGCCATTGCCGCCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGCAACCCGGCCACCAAGAAGAACACCGGCAACTGGCGTGCCTGCCCCTACATCCTCGgtaagtaacaacatcttcctcgtcgattgccaagcttgttcgtctccattgatggtgagatataagcgagtgaagtgactgatgtttgcaatggtttgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC