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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaagtacccctgtccataaaatattttaaatatttaggttctatttatgtattgaattttggtaagttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC

Basic information

species Oryza sativa
transcript LOC_Os06g40730.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 5
---tagaagtacccctgtccataaaatattttaaatatttaggttctattt-atgtat-tgaattttggtaagttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
   ||   | |       |   ||||||| || |   ||||  || |  || || ||| || |||||| ||  ||| | | || || |||     ||  || ||| || || |||||||||||||||||||||||||| ||  ||||| |||| ||||||||| ||||| |||||||||||||||||||||||||||| ||||||
cggtacttgcatttaacgctgcaaaatatcttga---tttaaattattcttgatatatgtgcattttgatat-ttcatgacaatttgtgttatgtctgctg-cagTCTGCTATATGGAGCAGAAGACCCCTCAATTGCTGGCATGGTTCTGGATAGTGCTTTCGCTAACTTATATGACTTAATGATGGAGCTTGTAGAAGTTTAC

upper sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
--tagaagtacccct-gtccataaaatattttaaatatttaggttctatttatgtattgaattttggta-agttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
  |  || ||  |||  || ||   || | |  ||| | || ||   || ||||     |  | | ||| |||| ||  | |||| ||              ||||| || |||||||| |||||||| || ||||| ||  |||| ||||| ||||| || || ||| |||||||  |||||||||||||||  ||||| || 
tgttaaaatatacctcatctattctatgtgtgtaat-tataagtcacatatatgag--aatctctagtatagttatttctcactt-tgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT

upper sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
-tagaagtacccctgtccataaaatattttaaatatttaggttctatttatgtattgaattttggt--aagttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
 | |   ||||  |   |   | | || |  ||| | |  |      |||| |    || | | ||  || |   |  |  ||| |         |     || || || |||||||| |||||||| || ||||| ||  |||| ||||| ||||| || || ||| |||||||  | |||||||||||||| |||||||| 
atggtcttacctttactctgtatacatgt--aat-tatgagccacccttatattcacaactctagtttaattgtctattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT

upper sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 6
tagaagtacccctgtccataaaatattt-taaatatttaggttctatttatgtattgaattttggtaagttcttcataacttctgtccaaacttttg----acagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
      |   |||  |  ||     | | ||| || |||    | |   || |||| || |||      |  || |  | | |  |  |   |  ||      || || || |||||||| |||||||| || ||||| ||  |||| ||||| ||||| || || ||| |||||||  | |||||||||||||| |||||||| 
-----atggtcctacctttactccgtatataagtaattattagccacccatatattcaaatttctagtttaattgactattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT

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|58669214|gb|CK057900.1|CK057900
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCA
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCA
EST: gi|33676219|gb|CF304458.1|CF304458
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTNTGGACAG
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
EST: gi|58694815|gb|CK083502.1|CK083502
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
EST: gi|29680364|gb|CB676639.1|CB676639
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCTATTGCCGGTCTGGTTTTGGACAG
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
EST: gi|58686455|gb|CK075142.1|CK075142
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
EST: gi|58671343|gb|CK060029.1|CK060029
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGG
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGG
EST: gi|58653936|gb|CK042616.1|CK042616
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAG
EST: gi|58668855|gb|CK057541.1|CK057541
EST:     GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG                         CCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTAGGACCA
genomic: GAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGAC-A

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: 67 (upstream exon), 74 (downstream exon)
Score: 28

AAACAGGATCTCAAATGCGCGGTGTCCTTTTTGCGAAACAATAAGGAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAGgtatttggtt ... cttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgtattgaattttggtaagttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
                           tcataac  putative branch site (score: 28)
                                             ctttt  putative PPT
      tattgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaagtacccctgtccataaaatattttaaatatttaggttctatttatgtattgaattttggtaagttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - cataaaa
- - - - - - - - - - - - - - - - - - - - - - - -tatgtat