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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGAGCCCTTCTTCAATGCAGCGGCTACCCAGTTTGTCCTTGGACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattccttaattaagacttcacattaatttagcagtaaactaaaaggattaaaaatatattgatcaatttaatttgaccatgctttctttgttatgat...

Basic information

species Oryza sativa
transcript LOC_Os01g13770.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13770.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 6
CTCTGGAGCCCTTCTTCAATGCAGCGGCTACCCAGTTTGTCCTTGGACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattccttaattaagacttcacattaatttagcagtaaactaaaaggattaaaaatatattgatcaatttaatttgaccatgctttctttgttatgat
||||||||||||||||||  ||||| ||||| |||||| |||||||||||||||||||| |  |||| ||| | |||||||||||||| ||  | ||||  |  |    | ||      ||| |  | |  | ||| |  || |   ||   |   |  |||||  | || ||  |                    
CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGCAAGTTCCCTTCTCTCTGTGGCTTTCTCTTGCCCCTGTTGTCATCGgtatgtaatc--ctcagttcgatcatcatctcataattaatcctaatgctctagcta---agcgatcacatgaaattacctgccag--------------
















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|84117005|gb|CD150772.1|CD150772
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|313084102|gb|HO213885.1|HO213885
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29613763|gb|CB618776.1|CB618776
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29671609|gb|CB667884.1|CB667884
EST:     CCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: CCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29616222|gb|CB621234.1|CB621234
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29643944|gb|CB648951.1|CB648951
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|25797136|gb|CA753097.1|CA753097
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29661884|gb|CB658159.1|CB658159
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
EST: gi|29657881|gb|CB654156.1|CB654156
EST:     ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTG                         GTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA
genomic: ACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCA

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: 73 (upstream exon), 72 (downstream exon)
Score: 111

CTCTGGAGCCCTTCTTCAATGCAGCGGCTACCCAGTTTGTCCTTGGACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattcctt ... agattaccagGTGTTTCAATGGCATCACTGACTGAACTTTCATTTAACTGGACGGGCTTCATCAATGCTATGATCTCTAACATCTCATTCACTTACCGGAGCATTTATTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGAGCCCTTCTTCAATGCAGCGGCTACCCAGTTTGTCCTTGGACAGCAAGTTCCCCTGCCTCTTTGGTTGTCTCTTGCCCCTGTCGTGCTTGgtaattccttaattaagacttcacattaatttagcagtaaactaaaaggattaaaaatatattgatcaatttaatttgaccatgctttctttgttatgat

- - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata