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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGAGCAAGAAGGAAAAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggataccagattttcttaagctgaagaattatgtctaataacggtgtctctagtgacactggtttccatcagtaattcaggtcttatacctgtt...

Basic information

species Oryza sativa
transcript LOC_Os08g42410.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 9
ATAGAGCAAGAAGGAAAAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggataccagattttcttaagctgaagaattatgtctaataacggtgtctctagtgacactggtttccatcagtaatt-caggtcttatacctgtt-----
||||||| | |||| |||||||| || || || ||||||||||| ||||| |||||||| |||||||||||| || ||||||| |||| || || | | | | | || | | || || || ||| | | | ||||| | ||
ATAGAGCGACAAGGGAAAGATGTCACTATCACTGCATTCTCCAAAATGGTGGGATATGCCCTTCAGgtgtgttgagtgcagattt-cttaggccgatggaagaattttgtcaatgct-----tatacgtgttgacttacattattgtccatacaatttatagttatttgaat
















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|33824375|gb|CF338004.1|CF338004
EST:     AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAG                         GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
EST: gi|87020958|gb|CI269675.1|CI269675
EST:     AAGATGTAACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAG                         GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
EST: gi|38472326|gb|CF956457.1|CF956457
EST:     AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAG                         GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
EST: gi|218484233|gb|FG953202.1|FG953202
EST:     AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAG                         GCTGGAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGGTGATCAATC
genomic: AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAGGTGATCAATC
EST: gi|33824376|gb|CF338005.1|CF338005
EST:     AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAG                         GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
EST: gi|29614435|gb|CB619448.1|CB619448
EST:     AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAG                         GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
genomic: AAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
EST: gi|38475005|gb|CF959138.1|CF959138
EST:     GATGTTACAATTACCGCATATCTCCAAGATGGTCGGATAATGCTCTTCAG                         GCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG
genomic: GATGTTACAATTACCGCAT-TCTCCAAGATGGTCGGAT-ATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG

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: 66 (upstream exon), 39 (downstream exon)
Score: 39

ATAGAGCAAGAAGGAAAAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggat ... caaatttcagGCTGCAGAGATACTTTCCAAGGAGGGAATCAGTGCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGAGCAAGAAGGAAAAGATGTTACAATTACCGCATTCTCCAAGATGGTCGGATATGCTCTTCAGgtgtgtggataccagattttcttaagctgaagaattatgtctaataacggtgtctctagtgacactggtttccatcagtaattcaggtcttatacctgtt

- - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - AAGATG