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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATGGAAGATGAGTTAGAAGAAACTGAGATAGAAGGCTTTGATGCGCAGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttttaatcactgcttcgttcatttttgttgcatttcttgtaagtaatacatccatgaatttgtggggtatggaatttgaaggaaccctatttg...

Basic information

species Oryza sativa
transcript LOC_Os05g51480.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51480.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G430027_T01 (Zea mays), 5'ss of exon 1
GAACATGGAAGATGAGTTAGAAGAAACTGAGATAGAAGGCTTTGATGCGCAGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttttaatcactgcttcgttca-tttttgttgcatttcttgtaagtaatacatccatgaatttgtggggtatggaatttgaaggaaccctatttg---
|||||||||||||||  | ||||| || |||||||| || |||||||| || ||||||||  |||||||||||||||| |||||||| || ||||||||||||||| || |||| ||   || ||  | ||||| ||||||||     |  ||  |         | |  |    |||    | || |  ||     |  |   
GAACATGGAAGATGAACTTGAAGAGACCGAGATAGAGGGGTTTGATGCACAAACTCAGACCCTGTTTTGTCAAAATGCGATCAATGACCTTCTTATACAGgtgcctgttctaatgaccattttgtcaaatttttcttgcatttaacacac-taccatgctagcagactattattctatc---tgtgcattaatttagtaaggta

upper sequence: LOC_Os05g51480.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 13
GAACATGGAAGATGAGTTAGAAGAAACTGAGATAGAAGGCTTTGATGCGCAGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttttaatcactgcttcgttcatttttgttgcatttcttgtaagtaatacatccatgaatttgtggggtatggaatttgaag--gaaccctatttg
|||||||||||||||  ||||||| ||||||||||| || |||||||| || ||||| ||| |||||||||| ||||| ||||||||||| ||||||||||||| | || |||       || | |   |   |    |||| | ||   |  |   |  ||    || | |    |  | | | ||   || ||  | |||
GAACATGGAAGATGAACTAGAAGAGACTGAGATAGAGGGGTTTGATGCACAAACTCAAACTCTGTTTTGTCAGAATGCGATCAATGATCTTCTTATACAGgtgcttgttctaagggggtgtttggtttctagcgactaatttttagtccct--tcattttattctattttagttcctaaactgtaaaatagatcctaaattg

upper sequence: LOC_Os05g51480.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 13
GAACATGGAAGATGAGTTAGAAGAAACTGAGATAGAAGGCTTTGATGCGCAGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgt-gccttttttaatcactgcttcgttcatttttgttgcatttcttgtaagtaat-acatccatgaatttgtggggtatggaatttgaaggaaccctatttg
|||  | ||||||||||| ||||||||||||||||| || ||   | | ||    ||||||||||| || ||  ||||  |  ||||||  ||  |||| || | |||| |||||    |  |  |  ||| || ||   | | |  |  | | | | ||  || |||||            |    || |  | | |    
GAATCTTGAAGATGAGTTGGAAGAAACTGAGATAGAGGGTTTCTGTTCTCAAGTGCAGACTTTGTTCTGCCATGATGCTGTTTATGATCAACTAGTACAAgtaggctttcttaatttgggtgttttatattatttttttctgtataatttggattgatattaataaatttccttaacgaatcaacccaaagtgcaccaaa--

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|58668330|gb|CK057016.1|CK057016
EST:     AGACTCAGACTTNG-TTTGTCAAAATGCCATCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29630334|gb|CB635343.1|CB635343
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCCCCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29669278|gb|CB665553.1|CB665553
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29634960|gb|CB639969.1|CB639969
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAA                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|29632887|gb|CB637896.1|CB637896
EST:     AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAG                         GTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
EST: gi|87009621|gb|CI309142.1|CI309142
EST:     AGACTCAGACTTTGTTTTGTCAAATTGCCATCAATGATCTGCTTATACAG                         GTTGCTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG
genomic: AGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTG

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: 61 (upstream exon), 73 (downstream exon)
Score: 34

GAACATGGAAGATGAGTTAGAAGAAACTGAGATAGAAGGCTTTGATGCGCAGACTCAGACTTTGTTTTGTCAAAATGCCATCAATGATCTGCTTATACAGgtgccttttt ... tcaatgacagGTTACTGCTAATTCTGTTCGTCTGGTTAGTTGTACCTCTCGGGAGCTAGTGGATCAATGGAATGCACCAGAAGGATTTTCAGTCAATGTTGCATCAGCTA




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