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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTTAAACAACTCTTTGGATGTGAAAGTCTAACTGCCGTGAGTGTTTCGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatttcctttcagaacaacatcatgtattgagacttgcactggttagtgtttgctagatgacatccatccctgcttgcaactcctagttagtat...

Basic information

species Oryza sativa
transcript LOC_Os08g39310.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39310.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G332809_T01 (Zea mays), 5'ss of exon 11
AAAACTTAAACAACTCTTTGGATGTGAAAGTCTAACTGCCGTGAGTGTTTCGGAG-TTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt---tcctttcagaacaacatcatgtattgagacttgcactggttagtgtttgctagatgacatccatccctgcttgca--actcctagttagtat
|| |||||||||||||||||| |||||||||| || || |||| |||||| ||||| ||| | ||||||| || |||| ||| ||| ||| |||||||||||| | || ||| | || | | || || ||| | | | || | | || | | ||| | | |||
-AAGCTTAAACAACTCTTTGGACGTGAAAGTCTTACCGCTCATGGTGTCTCGGAGGTTGCTTTCAGACCACCTTTACACGCAATCTACCAATATCTGACTGgttagttaccggactttctcttggcaaacgtttcccttcctagtcgcgcttgttggagaatttcagtcgtctgccttttggccctgctttgccctctgtt-----
















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|29643650|gb|CB648657.1|CB648657
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTTTAACTG                         ATGAATCGTCTTACTGGACTTTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|88227196|gb|CI228309.1|CI228309
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|87026983|gb|CI259636.1|CI259636
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|86421229|gb|CI057218.1|CI057218
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|29643027|gb|CB648034.1|CB648034
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|29619019|gb|CB624031.1|CB624031
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|29682543|gb|CB678818.1|CB678818
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTACGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|29667306|gb|CB663581.1|CB663581
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|29657921|gb|CB654196.1|CB654196
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
EST: gi|29619017|gb|CB624029.1|CB624029
EST:     CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTG                         ATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC
genomic: CGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGC

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: 75 (upstream exon), 75 (downstream exon)
Score: 31

AAAACTTAAACAACTCTTTGGATGTGAAAGTCTAACTGCCGTGAGTGTTTCGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatt ... tgttttgcagATGAATCGTCTTACTGGACTCTAGTTGGTCTAACACCCTGGTAGTAGGCGCTGATGAAACAACAGAAAATGCTGAAAGTGTTTATTCTATGCTTTGTATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACTTAAACAACTCTTTGGATGTGAAAGTCTAACTGCCGTGAGTGTTTCGGAGTTGCTGTCACAACACCTTTTCAAGCAACCTAACAAGCTCTAACTGgttagttatttcctttcagaacaacatcatgtattgagacttgcactggttagtgtttgctagatgacatccatccctgcttgcaactcctagttagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatccc