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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattttctttcctgtattcagcacaggattgttcttttaatatgttcttctgggatatttaaatgtcatattccatctcaagatattcacaattgaacttactgtgtttttcttctgcccttccatttgttgataagttttattaactgcaacctcatttgatgttctgcttacgtttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGA

Basic information

species Oryza sativa
transcript LOC_Os05g34540.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G435373_T02 (Zea mays), 3'ss of exon 9
gttaattttcttt---cctgtattcagcacaggattgttcttttaatatgttcttctgggatatt--taaatgtcatattccatctcaagatattcacaattgaacttactgtgtttttcttctgcccttccatttgttgataagttttattaactgcaacctcatttgatgttctgcttacgtttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGA
|| |||  ||| |    |   ||||   |  |  | ||  ||   ||      | ||   || ||  || ||| ||   |   |  |   |  ||     ||    |          |  ||||     |       |       ||||  ||| |     |||||||  ||   | ||   |||| | |||||||||||||||| || | |||||  || || |||||||| ||||||||||| ||  | || |||||||| || ||||| || || ||||||||||| ||||
gtgaatactctgtatgtccacattctaaagggcttggtcattgcgatgccaaatacttatattttgctagatggcaagctaatttactgaactttttttgttcccatcttgagaaggtatttctaattatatggccttctggtgcttttgctaaattttctctcattttttgccatcctattgtttctaaacagGTTAGGAAGATTGGTAGAGTTGTTCGTGCAATTGCTATCATGAGCCACCCAATCCCTAATACAAATGAGTCCCACTCGGTTCAAATTATTTTGCCTCAGA
















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|218498467|gb|FG951780.1|FG951780
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|29674550|gb|CB670825.1|CB670825
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|29689602|gb|CB685877.1|CB685877
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|396941200|gb|HO188409.1|HO188409
EST:     TTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: TTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|38471265|gb|CF955396.1|CF955396
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|702923|gb|D49214.1|D49214
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|58592473|gb|CF990781.1|CF990781
EST:     ACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: ACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|4880961|gb|AU065260.1|AU065260
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
EST: gi|218500069|gb|FG955684.1|FG955684
EST:     CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAG                         GTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG
genomic: CTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCG

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), 72 (downstream exon)
Score: 109

TGAATTTGATATGGAAGGGAAAGTCTGCGGCGTTACATCAGAAGGAGAAACTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttc ... ttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataagttttattaactgcaacctcatttgatgttctgcttacgtttattaacagGTTAGGAAGATAGGAAAAGTTGCACGCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGA
      ttttattaact  TA-rich tract