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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaatgccttttagtttacgtgttatttttaatattatctagtgtgcatgtatttgtgttaatttctgaagttatgcgtgagatcttttgtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAGGCAAAGAAGGTGCCAGCCAAAACTTTTACTCCTGGACAGGTGGTGGATG

Basic information

species Oryza sativa
transcript LOC_Os02g13990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G021742_T01 (Zea mays), 3'ss of exon 4
atgaatgccttttagtttacgtgttatttttaatattatctagtgtgcatgtatttgtgttaatttctgaagttatgcgtgagatcttttgttt---ttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAGGCAAAGAAGGTGCCAGCCAAAACTTTTACTCCTGGACAGGTGGTGGATG
   |        |  |||   ||  || |||   |||||| ||| ||||  | || |  || ||||||||  || |  | ||||| |||| |||   |||||||||||| |||| |||||  | ||||| ||||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| | |   |  | | 
-acaccatggaatgctttgtctggcatgttttccattatccagtctgcaaatgtt-gcttttatttctgattttct-tgggagattttttttttgctttgtagGAGAGAGTTGCGGCAGCGAAAAAGTTCCACTCAAAGGAAGCAGAGGAAGAGGCAAAGAAGGTGCCTGCCAAAACGTTTACTCCTGGTCTGCCTGATGCTC
















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|226698493|gb|GO497071.1|GO497071
EST:     ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAATTGCCGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatg ... gtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
EST: gi|29660695|gb|CB656970.1|CB656970
EST:     ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatg ... gtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
EST: gi|27553936|gb|CA997836.1|CA997836
EST:     ATAAATTGAAGCATTTGCGGTTGTTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatg ... gtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
EST: gi|29663404|gb|CB659679.1|CB659679
EST:     ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatg ... gtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
EST: gi|29663405|gb|CB659680.1|CB659680
EST:     ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAG                         GAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG
genomic: ATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatg ... gtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAG

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: 72 (upstream exon), 69 (downstream exon)
Score: 50

ACTTGATAATACTGTAACCAAGCAGCCAGACTACCGGTTGTATGTGATCCATAAATTGAAGCATTTGCGGTTGCTGGATTTCAAGAAAGTGAAACAACAGgttagcaatg ... gtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAGGCAAAGAAGGTGCCAGCCAAAACTTTTACTCCTGGACAGGTGGTGGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtatttgtgttaatttctgaagttatgcgtgagatcttttgtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAGGCAAAGAAGGTGCCAGCCAAAACTTTTACTCCTGGACAGGTGGTGGATG
            tgttaat  putative branch site (score: 50)
                                       tcttttgtttttgt  putative PPT
      tatttgtgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaatgccttttagtttacgtgttatttttaatattatctagtgtgcatgtatttgtgttaatttctgaagttatgcgtgagatcttttgtttttgtagGAGAGAATTGCAGCAGCACAGAAGTTTCACTCAAAGGAGGCAGAGGAAGAGGCAAAGAAGGTGCCAGCCAAAACTTTTACTCCTGGACAGGTGGTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
-tgaatgc
- - - - - - - - - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcgtg