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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgcatttaagttttgctgggattctggggttatgttttgtatcgttcgtggagaactgagttcattttagtctgagcaataattttatggaat...

Basic information

species Oryza sativa
transcript LOC_Os11g35710.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g35710.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G468929_T01 (Zea mays), 5'ss of exon 15
----------------ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgcatttaagttttgctgggattctggggttatgttttgtatcgttcgtggagaactgagttcattttagtctgagcaataattttatggaat-------
                || ||||| |||||||||||||| ||||||||||| |||||  | |||||||||||| |||||||||||||||| || ||||||||| |||  ||||| | |  ||  |   |        | | |     ||   | || || |      ||   | ||     || | ||| ||| | |  |       
TACACCTTCATACCAGATTGAGCGTGATCCAGCACCACTACATCGTGCTGCGAAAGAGCTGATCAATATGCAGATGGAAACAGGAGAGTTTCCACAACAAgtaggtttccattttattagtgtcgaagt------aatctatcgcagataagt-gttgatatagtctttgtctctacaacaagaagtaaatttgttgtgtttctttt

upper sequence: LOC_Os11g35710.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G006937_T01 (Zea mays), 5'ss of exon 17
ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgcatttaagttttgctgggattctggggttatgttttgtatcgttcgtggagaactgagttcattttagtctgagcaataattttatggaat-
 | || || |||||| | ||| | |||||||||||||| ||||| ||||| |||||  |||| ||||||||||| || || |||||||| || ||||    ||| | ||  | |      |||| || |  |    |          |  |||| | ||  | || |    || |||||  |   
TTTGAACGAGATCCAACGCCATTACATCGTGCTGCAAAGGAATTGATCAACATGCAACTGGAGACAGGAGAGTTTCCTCAGCAAgtaagctc-cattctgttttcgttgatagtagtacattatattgttgacaagtgaaaactcgttctgttcctcttgatttgtgtttcaaatttatccagag
















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|86844024|gb|CI336718.1|CI336718
EST:     CAAAAGAATTAATCAATATGCAGTT-GAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|86885403|gb|CI318554.1|CI318554
EST:     CAAAAGAATTAATCAATATGCAGGTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATTTTGGAGCCTTCAATCCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|86874705|gb|CI318264.1|CI318264
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|29639294|gb|CB644303.1|CB644303
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|88483123|gb|CI420394.1|CI420394
EST:     TGCAGTTGGAAACAGGAGAGTTCCCCCCACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: TGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|88837630|gb|CI078990.1|CI078990
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|88503306|gb|CI430812.1|CI430812
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|86853796|gb|CI329242.1|CI329242
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATATTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|29631086|gb|CB636095.1|CB636095
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|88244547|gb|CI243669.1|CI243669
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCGACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTGTTCTTGAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|86871672|gb|CI331049.1|CI331049
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|86838894|gb|CI330320.1|CI330320
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|87009292|gb|CI313765.1|CI313765
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|58691093|gb|CK079780.1|CK079780
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
EST: gi|29636672|gb|CB641681.1|CB641681
EST:     CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAA                         GAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC
genomic: CAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTAC

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: 70 (upstream exon), 73 (downstream exon)
Score: 40

ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgc ... tcttaattagGAACATGTTGGAGCCTTCAATGCATGCCTCTTCTTTAATTACCCCAACTACCGCAACTTATTCCCTATCTGGGCTCTTGGAGAGTACTGTCGTCATCTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAGCGGGATCCAGCACCACTGCATCGTGCTGCAAAAGAATTAATCAATATGCAGTTGGAAACAGGAGAGTTCCCCCAACAAgtaagttcgcatttaagttttgctgggattctggggttatgttttgtatcgttcgtggagaactgagttcattttagtctgagcaataattttatggaat

- - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA