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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAAGCTCTTTTTGATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatatacacgcttcattctacaattttctttggcttgttatattgtttctgctgctgttcaactgaatcagcgcacacaatattctattttcttatcaagtttacctgttatattgcttag

Basic information

species Oryza sativa
transcript LOC_Os03g58700.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G825524_T02 (Zea mays), 5'ss of exon 13
ATTGAAGCTCTTTTTGATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaa-tatacacgcttcattctacaa-----ttttctttggcttgttatattgtttctgctgct----------------gttcaactgaatcagcgca-cacaat---attctattttcttatcaagttt-----acctgttatattgcttag------------
||||| || || || ||||||||||| || || ||||| |||||||||||||||||| ||||||| || | |  | || |||| ||  | ||     ||||   | | ||||| | ||  |||||| |||                ||||| ||  |||||| || |||| |   |||  ||||||| || ||||||     |||||| | | || ||              
ATTGAGGCACTATTCGATTTAATTAAGGGGCTGATAAAGGATATGGATGGGGCTCAAGATGATGAAgtgagttcatacacttcgttagaaaagcgaatttttacttgtttgttgtcttcattctgccgcttagtgctcccaatattgttcagctagatcagcacaacacatttcaatttcattttctcatgaagtttgctcaacctgtaacaatgtttttttattattttag

upper sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 14
ATTGAAGCTCTTTTTGATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatat-acacgcttcattctaca-----attttctttggcttgttatattgtttctgctgct----------------gttcaactgaatcagcgcacacaatattctattttcttatcaagtttacctgttatattgcttag------------------------------
||||| || || || ||||||||||| || || ||||| ||||||||||| |||||| |||||||||| | || | || |||  ||  | |     | |||   | | ||||| | ||  ||||| ||||                ||||| ||  |||||  || |||   ||| |||   || |||  ||  | ||   | ||||| |                               
ATTGAGGCACTATTCGATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcatacactttgttagaaaggtgaaattttacttgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtacaaacacatttcaattccattttcattttctcatgaagt-ttgctcaacttgtaacaatgttcttttaattattttag
















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|58612508|gb|CK040220.1|CK040220
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|29621778|gb|CB626789.1|CB626789
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|29622156|gb|CB627167.1|CB627167
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|58685652|gb|CK074339.1|CK074339
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|29686657|gb|CB682932.1|CB682932
EST:     ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|29613031|gb|CB618044.1|CB618044
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|29616228|gb|CB621240.1|CB621240
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|58678521|gb|CK067208.1|CK067208
EST:     ATTTAATTAAAGGGCTTATAAAAGATATGGATGGGGCTCAAAATGACGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
EST: gi|33677499|gb|CF305738.1|CF305738
EST:     ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAG                         CTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT
genomic: ATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATT

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: 66 (upstream exon), 73 (downstream exon)
Score: 56

ATTGAAGCTCTTTTTGATTTAATTAAAGGTCTTATAAAAGATATGGATGGGGCTCAAAATGATGAGgtaatataca ... tattgcttagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATTCACATGTTGCACAATGATGACCATGAAGAGATGTTGAAG




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