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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgtactagctgtgtacacatgtttgggaaagaaacatacttgcatagaattaccttgattatttcacaggagtcccttttaatgaacaccttgttttctagataagtgtataccagatacatgctgatatatatttctgttatacagtcagtgaagtttgatgtacttacctgtgggtcttctctctgtag

Basic information

species Oryza sativa
transcript LOC_Os09g33500.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 9
CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgtac--tagctgtgtacacatgtttgggaaagaaacatacttgcatagaattaccttgattatttcacag--gagtcccttttaatgaacaccttgttttctagataagtgtataccagatacatgctgatatatatttctgttatacagtcagtgaagtttgatgtacttacctgtgggtcttctctctgtag
 ||||||||||| |||||  ||||||||||||||||||||||||||||    || || ||||||||||| ||||||||||||    | | ||  ||    ||| |||||| ||       ||   || || ||  |  || | || ||    |      ||| | || |   |                                                                                                     
TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtgtcttgggtgcatatgggtgtatgggaaggaggttcgtttaggtacaactatttccataagtttacccttggacggttttgagtggagttc-----------------------------------------------------------------------------------------------------

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 3
CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgtac--tagctgtgtacacatgtttgggaaagaaacatacttgcatagaattaccttgattatttcaca--ggagtcccttttaatgaacaccttgttttctagataagtgtataccagatacatgctgatatatatttctgttatacagtcagtgaagtttgatgtacttacctgtgggtct--tctctctgtag
 ||||||||||| |||||  ||||||||||||||||||||||||||||    || || ||||||||||| ||||||||||||    | | ||  ||    ||| |||||| || |     ||   ||| | ||  |  || | || ||   ||  |   ||| | || ||  | | |            ||  | | | |    |    || |  |||||||   || | |   |||  |    || ||||  ||||||| ||  ||| |||||||
TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAGgtatgttgtgtcttgggtgcatatgggtgtatgggaaggagattactttaggtaggactatttctataagtttaccttgggatggttttgagtggacttcctat------------tgctttcaaaacggctctccatttccatttctggattatact---tgatatcatctgcacttcactgtgggcctcatctttctgtag
















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|86600093|gb|CI258433.1|CI258433
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|87032949|gb|CI187573.1|CI187573
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|88219808|gb|CI219368.1|CI219368
EST:     CCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|86494245|gb|CI136878.1|CI136878
EST:     TAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: TAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|58687862|gb|CK076549.1|CK076549
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATGGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGAT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGAT
EST: gi|29637529|gb|CB642538.1|CB642538
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|33800162|gb|CF325945.1|CF325945
EST:     AGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: AGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|33380822|gb|CF196165.1|CF196165
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|86542747|gb|CI182953.1|CI182953
EST:     TTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: TTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|157649975|gb|EX449609.1|EX449609
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|87022122|gb|CI259194.1|CI259194
EST:     CGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|2312022|gb|C28177.1|C28177
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|29645720|gb|CB650727.1|CB650727
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|89169219|gb|CI038726.1|CI038726
EST:     GCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: GCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|87034409|gb|CI189033.1|CI189033
EST:     TCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: TCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|33666828|gb|CF297795.1|CF297795
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|29657623|gb|CB653898.1|CB653898
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|27576086|gb|CA998780.1|CA998780
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTT
EST: gi|86497317|gb|CI139950.1|CI139950
EST:     CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG                         ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCCAAGATGGT
genomic: CTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACT-CCAAGATGGT

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), 71 (downstream exon)
Score: 172

CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgta ... ctctctgtagATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAGgtatgttgtactagctgtgtacacatgtttgggaaagaaacatacttgcatagaattaccttgattatttcacaggagtcccttttaatgaacaccttgttttctagataagtgtataccagatacatgctgatatatatttctgttatacagtcagtgaagtttgatgtacttacctgtgggtcttctctctgtag

- - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG