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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaacataatttttcctttgaaattccttccggttattatcttttgttttattggcttatatttccttttctgcttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G045241_T05 (Zea mays), 5'ss of exon 15
AATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaacataatttttcctttgaaattccttc--cggttattatcttttgttttattggcttatatttccttttctgc-ttgtag---------------
 | ||||| |||||||||||||||||||||||  | ||||||||||| ||      ||||||||||||||| ||||| |||||||||||| ||||||||||||| | |   | ||| || | |||  |||         |  | |  |||  | ||   |||       | || ||   | |||                  
GAACCAAGATTGGAACTGAACCTGTGGGATTTCAGCACAGAACCTGATGATTGTGTCCTTGATTTAACTCTCAGTCTGAAGCCAAGTTTTTCTGGAACAGgtgcgtga---attttatcttgtgaggttcaagaaatactcgtcacttttcatcttgccggccgtggcatgctgtttcacattgctatttttcgtattgcag
















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|29613120|gb|CB618133.1|CB618133
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29644979|gb|CB649986.1|CB649986
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|89167683|gb|CI018289.1|CI018289
EST:     AAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29663527|gb|CB659802.1|CB659802
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     AACTACCCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AACTA-CCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29638287|gb|CB643296.1|CB643296
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29656192|gb|CB652467.1|CB652467
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29613155|gb|CB618168.1|CB618168
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|33801021|gb|CF326384.1|CF326384
EST:     TGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: TGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29633044|gb|CB638053.1|CB638053
EST:     AAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29613395|gb|CB618408.1|CB618408
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29628841|gb|CB633852.1|CB633852
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|8856640|gb|AU093958.1|AU093958
EST:     AACTACCTTGGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AACTACCTT-GATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG

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: 55 (upstream exon), 75 (downstream exon)
Score: 37

AATCCAAGGTTGGAACTGAACCTGTGGGATTTTGGTACAGAACCTGAGGACAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG




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