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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttgttccattactatgtgtcctcatttctgtcccagataactttgctgcatactgaacatttatttcttttgttttcgttatgttaatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG

Basic information

species Oryza sativa
transcript LOC_Os01g54560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54560.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G123277_T01 (Zea mays), 3'ss of exon 2
------taaatttgttccattac-tatgtgtcctcatttctgtcccagataactttgctgcatactgaacatttatttcttttgttttcgttatgttaatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG
      ||   || || | || | |   || | ||| ||   | |  |   | ||   ||  ||    | | | | |||||||||| |        |||| ||||||||||||||||||||| |||| || |||| |||||| |  ||| |||||||||| |||||||||||||| || ||||| ||||| || ||||| ||||| |
gattgatatggtttttaccttgcatgattgacttcacttagtttcttg--tatttacttgtgtaaattaaaatgagttcttttgttgt----gcactaat-ctgcagGGAGTAAGCAAGGGAATAGTTGCCGAGAGGATACTTGCATCAGTGAAGGAGAGGGGAAAGCAGGCTGATTTCGTATTGTGCATCGGCGATGATAGGTCCG

upper sequence: LOC_Os01g54560.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G304274_T01 (Zea mays), 3'ss of exon 2
------taaatttgttccattactatgtgtcctcatttctgtcccagataactttgctgcatactgaacatttatttcttttgttttcgttatgttaatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG
      ||   || || | || |    |   || |  |  ||  |   ||  ||   ||  ||    | | | | |||||||||| |        |||| ||||||||||||||||||||| |||| || |||| |||||| |  ||| |||||||||| |||||||||||||| || ||||| ||||| || ||||| ||||| |
gatggatatggtttttaccttgcatgattgacttaacttagtttcttgta-tttatttgtgtaaattaaaatgagttcttttgttgt----gcactaat-ctgcagGGAGTAAGCAAGGGAATAGTTGCCGAGAGGATACTTGCATCAGTGAAGGAGAGGGGAAAGCAGGCTGATTTCGTATTGTGCATCGGCGATGATAGGTCTG

upper sequence: LOC_Os01g54560.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G118462_T01 (Zea mays), 3'ss of exon 2
------taaatttgttccattac-tatgtgtcctcatttctgtcccagataactttgctgcatactgaacatttatttcttttgttttcgttatgttaatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG
      ||  ||| || | || | |    | |||    |  ||  | | ||  |    || | | | ||   |   ||| |||||| |        |||| ||||||||| ||||||||||| |||| || |||| |||||| |  ||| ||||||||||||||||||||||||| ||  |||| ||||| || ||||| ||||| |
gattgatacgttttttaccttgcatgatcgacctttacttagtttctggtatttacagtgtaaattaaaa--tagattcctttgttgt----gcactaat-ctgcagGGAATAAGCAAGGGAATAGTTGCCGAGAGGATACTTGCATCAGTGAAGGAGAGAGGAAAGCAGGCTGATTTCTTATTGTGCATCGGCGATGATAGGTCTG

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|572443|gb|D41954.1|D41954
EST:     AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAN                         GGAGTAAGCAAGGGAGTAGTAGCTGAGA
genomic: AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGA
EST: gi|88234859|gb|CI232710.1|CI232710
EST:     AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTGGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|87031848|gb|CI272549.1|CI272549
EST:     ATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: ATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|86869341|gb|CI339065.1|CI339065
EST:     GTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: GTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|86858429|gb|CI273035.1|CI273035
EST:     AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|87037918|gb|CI192540.1|CI192540
EST:     GCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: GCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|87023217|gb|CI272045.1|CI272045
EST:     CCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: CCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|87040603|gb|CI195225.1|CI195225
EST:     TGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: TGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|86600818|gb|CI356575.1|CI356575
EST:     AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|86858264|gb|CI271140.1|CI271140
EST:     TCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTATCTGAGAAGATACTCGTCTCAAAGAAGGAG
genomic: TCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|87021398|gb|CI274005.1|CI274005
EST:     CCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: CCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|29630629|gb|CB635638.1|CB635638
EST:     AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
EST: gi|87038409|gb|CI193031.1|CI193031
EST:     AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAG                         GGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG
genomic: AACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAG

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: 70 (upstream exon), 75 (downstream exon)
Score: 28

CTCCCAGGCAAAGGAGTTACTTGATCATCTGGAAAGTGTATTAGCAAATGAACCTGTTTCTGTCAAAAGTGGCCAGTTCATTGTTGAAGTCAAACCTCAGgttagttcat ... aatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgctgcatactgaacatttatttcttttgttttcgttatgttaatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG
                                         tgttaat  putative branch site (score: 28)
               aacatttatttctttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatttgttccattactatgtgtcctcatttctgtcccagataactttgctgcatactgaacatttatttcttttgttttcgttatgttaatactgcagGGAGTAAGCAAGGGAGTAGTAGCTGAGAAGATACTCGTCTCAATGAAGGAGAGAGGAAAGCAGGCTGACTTTGTATTATGCATTGGTGATGACAGGTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - ctgtccc
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcatac