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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataacttgtgccatcgccatgccatcttttgaaaagtatttttgtgttctattattttctttcttggtactaacattttgcacatgtcgtaactcag

Basic information

species Oryza sativa
transcript LOC_Os01g68320.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G059020_T01 (Zea mays), 5'ss of exon 8
ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcg-aataacttgtgccatcgccatgccat--cttttgaaaagtatttttgtgttctattatttt---ctttcttggtactaacattttgcacatgtcgtaactcag
||||| ||||| |||||||||||||| ||||||||||| ||||| |||||||| ||| |||| || ||||||||||| || || || ||||||||||   ||  ||  ||  || |  ||    |   | ||  |  |   | |||| ||  |||  |||   |   | |  |  |||| ||| ||  || | ||||   ||
ATCCGCCCAGATAGGCAAACCTTGTACTGGAGTGCCACATGGCCTAGAGAAGTTGAAGCCTTAGCAAGACAATTTCTACAAAATCCTTACAAGgtgcacgatctctgctgttattgttattttctggttcttttattgccatgttgtattgaattgattttgacagcccttctcttaacttttagcttatattgtaatgtag

upper sequence: LOC_Os01g68320.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G362850_T01 (Zea mays), 5'ss of exon 7
ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcg-aataacttgtgccatcgccatgccat--cttttgaaaagtatttttgtgttctattatttt---ctttcttggtactaacattttgcacatgtcgtaactcag
||||| |||||||||||||||||||| ||||||||||| ||||| |||||||| ||| |||| || ||||| ||||| || || || ||||||||||   ||  ||| ||  || |  ||    |   | ||  |  |   | |||| ||  |||  |||   |   | |  |  |||| ||| ||  || | ||||  |||
ATCCGCCCAGACAGGCAAACCTTGTACTGGAGTGCCACATGGCCTAGAGAAGTTGAAGCCTTAGCAAGACAGTTTCTACAAAATCCTTACAAGgtgcacgatctcttctgttattgttattttctggttcttttattgccatgttgtattgaattgattttgacagcccttctcttaacttttagcttatattgtaatgcag
















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|29627565|gb|CB632576.1|CB632576
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29636635|gb|CB641644.1|CB641644
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29673236|gb|CB669511.1|CB669511
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29640324|gb|CB645333.1|CB645333
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29679220|gb|CB675495.1|CB675495
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29644134|gb|CB649141.1|CB649141
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|33797128|gb|CF324429.1|CF324429
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29638139|gb|CB643148.1|CB643148
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29675369|gb|CB671644.1|CB671644
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAC                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29675371|gb|CB671646.1|CB671646
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29645557|gb|CB650564.1|CB650564
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29666768|gb|CB663043.1|CB663043
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAGAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29677571|gb|CB673846.1|CB673846
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29669296|gb|CB665571.1|CB665571
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATA
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATA
EST: gi|29667787|gb|CB664062.1|CB664062
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
EST: gi|29670396|gb|CB666671.1|CB666671
EST:     CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAG                         GTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT
genomic: CAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATT

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: 108

ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataa ... cgtaactcagGTAATCATAGGATCACCTGATCTGAAAGCTAATCATTCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAAGTAGAATCCTTGGCTAGACAATTTCTGCAGAACCCATACAAGgtgcgaataacttgtgccatcgccatgccatcttttgaaaagtatttttgtgttctattattttctttcttggtactaacattttgcacatgtcgtaactcag

- - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG