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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacctggtttcgttgtcagggagcacaagtgattatttatttggctagcatgttttcagttgttacactacgcctgtctgatgtatgctattgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAAAAGGCTCGAGGAACTAGGTTGGGAGGAATATACCGAGCTATACTTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g10280.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10280.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G036123_T01 (Zea mays), 3'ss of exon 6
-----aacctggtttcgttgtcagggagcacaagtgattatttatttggctagcatgttttcag-ttgttacactacgcctgtctgatgtatgctattgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAAAAGGCTCGAGGAACTAGGTTGGGAGGAATATACCGAGCTAT--ACTTGAAG
     |     | ||| |  |||   ||| |     |  | | || |  ||| ||  ||| |||   || |||||       | ||  | ||  |||| ||| ||||| |||| | |||||| ||||||||||||| ||||| ||||||| |||| ||||||| ||||| | |||   |||||||| |    ||  |     ||||  
cttccatagctgcttcatgttcataaagcgcgt---agcagtcatatctctatcaattttccaggccgtcacactgtattgttgtg--gcattttatt-cttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACAGCAGAAAGGCTGGAGGACCAAGGCCCGGAGGAATTTCTGAAGGGAATGGATTGA--

upper sequence: LOC_Os01g10280.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G133121_T02 (Zea mays), 3'ss of exon 14
-----aacctggtttcgttgtcagggagcacaagtgattatttatttggctagcatgttttcag-ttgttacactacgcctgtctgatgtatgctattgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAAAAGGCTCGAGGAACTAGGTTGGGAGGAATATACCGAGCTAT--ACTTGAAG
     |     | ||| |  |||    || |     |  | | || |  ||| || |||| |||   || |||||   |   | ||  | ||  |||| ||| ||||| |||| | |||||| ||||||||||||| ||||| |||||||  ||| ||||||| ||||| | |||   |||||||| |    ||  |     ||||  
cttccatagctgcttcatgttcataatgcgcgt---agcagtcatatctctatcaagtttccaggccgtcacactgtactgttgtg--gcattttatt-cttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGAAAGGCTGGAGGACCAAGGCCCGGAGGAATTTCTGAAGGGAATGGATTGA--
















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|88264491|gb|CI368265.1|CI368265
EST:     TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|88490048|gb|CI427320.1|CI427320
EST:     TTATTGGCAGTTAGGATGGTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|86892278|gb|CI332277.1|CI332277
EST:     TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|88829350|gb|CI074220.1|CI074220
EST:     TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|88473885|gb|CI411156.1|CI411156
EST:     TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|89188813|gb|CI048549.1|CI048549
EST:     TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: TTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|88269589|gb|CI380887.1|CI380887
EST:     CAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: CAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
EST: gi|88463724|gb|CI527051.1|CI527051
EST:     GCTGGCCTCAAGAGATCCTGAGTTGGGGGACAA                         GGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA
genomic: GCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAA

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: 65 (upstream exon), 57 (downstream exon)
Score: 17

AAGGTATTCCTGTTGCTACTGTTGCAATTGGAAATGCGGAAAATGCAGGTTTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttc ... ttgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAAAAGGCTCGAGGAACTAGGTTGGGAGGAATATACCGAGCTATACTTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcatgttttcagttgttacactacgcctgtctgatgtatgctattgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAAAAGGCTCGAGGAACTAGGTTGGGAGGAATATACCGAGCTATACTTGAAG
                              gtctgat  putative branch site (score: 17)
                                             ttgctttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacctggtttcgttgtcagggagcacaagtgattatttatttggctagcatgttttcagttgttacactacgcctgtctgatgtatgctattgctttcagGGCAACTGAATACCAGCATGATCTGAGGGATATGGTGTTGGAGAAAGCAAAAAGGCTCGAGGAACTAGGTTGGGAGGAATATACCGAGCTATACTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - gcacaag
- - - - - - - - - - - - - - - - - - - - - -gctagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgtct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgc