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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaaccccatctctgatccgctctactctactctactgttcctccacacaaatccatgtgatggcggatggcctcctcgcgttagttcttgtttgcttcaatttcacgctgtcacacgtacgaggtggcggtgcag

Basic information

species Oryza sativa
transcript LOC_Os05g36270.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36270.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G322953_T04 (Zea mays), 5'ss of exon 1
ACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaaccccatctctgatccgctctactctactctactgttcctccacacaa-atccatgtgatggcggatg-gcctcctcgcgttagttcttgtttgcttcaatttcacgctgtcacacgtacgaggtggcggtgcag
 |||||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||    |  | |     | | |      ||||  | |  ||  |   ||  |||||      | |    | || | |||   | | ||  ||    |                                        
CCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCGCCGCGGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGAGAGACCAACGTCCAGgcaagca----cggcaccaccacacacacactgactcgcccgccccgacgatcaccatccactccgcgcctttcgtgcgtactctgctgaattactgagccccc--------------------------------------
















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|33679306|gb|CF307545.1|CF307545
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88574436|gb|CI666205.1|CI666205
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAG
EST: gi|88306899|gb|CI639319.1|CI639319
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGA
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGA
EST: gi|88354625|gb|CI678668.1|CI678668
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88434653|gb|CI690933.1|CI690933
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|29670800|gb|CB667075.1|CB667075
EST:     GGCCAGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: GGCC-GGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|29663073|gb|CB659348.1|CB659348
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88575554|gb|CI669699.1|CI669699
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTC
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTC
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88328095|gb|CI649896.1|CI649896
EST:     GGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGNTC-AG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCA
genomic: GGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACG-TCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCA
EST: gi|33684972|gb|CF313211.1|CF313211
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88329945|gb|CI652332.1|CI652332
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|33688486|gb|CF316725.1|CF316725
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|33683625|gb|CF311864.1|CF311864
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88309089|gb|CI654708.1|CI654708
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|86877142|gb|CI311444.1|CI311444
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCT
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCT
EST: gi|88325180|gb|CI646601.1|CI646601
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGA
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGA
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88332374|gb|CI656243.1|CI656243
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88575220|gb|CI669365.1|CI669365
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAG
EST: gi|33688998|gb|CF317237.1|CF317237
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|33686898|gb|CF315137.1|CF315137
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|33693501|gb|CF321740.1|CF321740
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
EST: gi|88592321|gb|CI710419.1|CI710419
EST:     AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAG                         GGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG
genomic: AGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAG

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), 75 (downstream exon)
Score: 35

ACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaacc ... ggcggtgcagGGTGAGGAGCAGAAGAAGCTTGACGTGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGCCTCGCCAAGCTCATCGGCCTCGCCGGCGACACCAACGTCCAGgcaagcaaccccatctctgatccgctctactctactctactgttcctccacacaaatccatgtgatggcggatggcctcctcgcgttagttcttgtttgcttcaatttcacgctgtcacacgtacgaggtggcggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA