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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctgttacacattaagtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT

Basic information

species Oryza sativa
transcript LOC_Os01g58380.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58380.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G106250_T01 (Zea mays), 3'ss of exon 3
gtcctgttacacatta----agtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT
||| ||| ||| |||| || | ||| || | | || | | | || | | | |||| ||||| ||||| | |||| || |||||| | || |||||||| ||||| ||||| || |||||||||||||||||||||||||| |||||||||||||| |||||||| || |||||
--ttgacaacagcttatgctagtctgaaatcgcatatctgtctattctataatatggatgttatcagacttgctagattgtctgatgttttttt--tttggcagACTCGGGAAGTCCGTTATATGCTCGCAAGATTACCCAGGATTCATCGTGAACCGCATCCTCATGCCGATGATCAACGAGGCCTTCTGGGCTCTGTACACC

upper sequence: LOC_Os01g58380.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G15290.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtcctgttacacattaagtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT
| | | || || | | | | ||| | | | | | | | | | | | || | || ||| ||| |||| | |||||| |||| ||||| | | |||||||||||||| | || ||| | |||||||| ||||||||||| |||||||| || |||||| ||||||||||
tagccttcttgtgt-ttgattgcgcggtt-taactaactaaatcgctgattcagttactctctttagatttaaatttaactgtatatccctgaaacctgcagGTTTGGCAAGACAACAGTCTGCTCACAAGACTATGCGGGATTCGTAGTGAACCGAATCCTCATGCCTATGATCAATGAAGCGTTCCACACACTTTACACA

upper sequence: LOC_Os01g58380.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ28731 (Selaginella moellendorffii), 3'ss of exon 3
gtcctgttacacattaagtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT
|| | || | ||| | ||| || | | | || || | || |||||||| | |||| | |||| ||| || ||| |||| ||||| ||||||||||| ||||||||||||||||||| || || |
-----------------------------------------------gtaagagagcagc-acccatcttatagaagctaagc-tgatcaccccggatagATTCGGCAAGACGGTGGTGAGCTCCCGCGACTTCCCGGGCTTCGTCGTCAACCGGATCCTCATGCCGATGATCAACGAGGCGTTCTACGCGCTGCTCGAG

upper sequence: LOC_Os01g58380.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ30692 (Selaginella moellendorffii), 3'ss of exon 3
gtcctgttacacattaagtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT
|| | ||| | ||| | | | || | | | || ||| | || |||||||| | |||| | |||| ||| || ||| |||| ||||| ||||||||||| ||||||||||||||||||| || || |
-----------------------------------------------gtaagaaagcagc-acccatcttagagaagctaagc-tgatcaccccggacagATTCGGCAAGACGGTGGTGAGCTCCCGCGACTTCCCGGGCTTCGTCGTCAACCGGATCCTCATGCCCATGATCAACGAGGCGTTCTACGCGCTGCTCGAG

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|29663173|gb|CB659448.1|CB659448
EST:     GCTGATACATCAGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAG                         GCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
genomic: GCTGATACATCAGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAGgtaactgaaa ... aaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
EST: gi|86596178|gb|CI266681.1|CI266681
EST:     GCTGATACATCTGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAG                         GCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
genomic: GCTGATACATCAGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAGgtaactgaaa ... aaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
EST: gi|86855103|gb|CI263170.1|CI263170
EST:     TTCACTAAAGTCAAATCTTTTTCTGAAAG                         GCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
genomic: TTCACTAAAGTCAAATCTTTTTCTGAAAGgtaactgaaa ... aaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
EST: gi|33675330|gb|CF303569.1|CF303569
EST:     GCTGATTCATCAGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAG                         GCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
genomic: GCTGATACATCAGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAGgtaactgaaa ... aaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
EST: gi|87020245|gb|CI261109.1|CI261109
EST:     GTTTTCACTAAAGTCAAATCTTTTTCTGAAAG                         GCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA
genomic: GTTTTCACTAAAGTCAAATCTTTTTCTGAAAGgtaactgaaa ... aaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAA

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: 41

ACTTTTTTAACCCTCCTCCGATAATGAAATTGATTGAAATCATACGTGGGGCTGATACATCAGAAGAGGTTTTCACTAAAGTCAAATCTTTTTCTGAAAGgtaactgaaa ... aaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT
                              gcctgat  putative branch site (score: 41)
 tgattatttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctgttacacattaagtttgaagccgtaaatccgttcaatgtaatgttggcaagtacttgtccacttgatattgcctgattatttttgaaccttgcagGCTTGGGAAGACGGTAATATGCTCACAAGACTACCCTGGTTTCATCGTGAACCGCATCCTCATGCCAATGATCAACGAGGCGTTCTGGGCACTTTACACT

- -ctgttac
- - - - - - - - - - - - - - - - -ccgttca
- - - - - - - - - - - - - - - - - - - - - - - tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcctg