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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATGGAGGACCACGTGCTGCTGAGTATTTGAAGGAAAATTTGTTCGAAAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttctctttgattcttacctttccagttctctgttcaccttttttttaaaggttgctaatgattattatcttctcaacttttgaaaaaaaaatcaaaacataacaacag

Basic information

species Oryza sativa
transcript LOC_Os02g15594.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15594.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G442404_T01 (Zea mays), 5'ss of exon 3
GTCATGGAGGACCACGTGCTGCTGAGTATTTGAAGGAAAATTTGTTCGAAAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttctctttgattcttacctttccagttctctgttcaccttttttttaaaggttgctaatgattattatcttctcaacttttgaaaaaaaaatcaaaacataacaacag
||||||| ||| ||||||||||||||||||||| |||  | ||||| || || ||||| || |||||||| ||| |||| |||||||||||||| ||||||| || |||||||    | |      |  ||   ||   |  || || || |    | | | |    ||  ||||| || |||||  |||   ||||                 
GTCATGGTGGATCACGTGCTGCTGAGTATTTGAGGGAGCACTTGTTTGAGAACCTTCTCAAGCACCCTGATTTCTTGACGGATACAAAGCTTGCTATAAgtatttcttctcttcagctgta----ctgtagacttcctgttgccattattgttggtgctacaacctgtt--tatctgctaaactt--gaatttaaaacag--------------

upper sequence: LOC_Os02g15594.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G073788_T02 (Zea mays), 5'ss of exon 3
GTCATGGAGGACCACGTGCTGCTGAGTATTTGAAGGAAAATTTGTTCGAAAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttctctttgattcttacctttccagttctctgttcaccttttttttaaaggttgctaatgattattatcttctcaacttttgaaaaaaaaatcaaaacataacaacag
||||||||||| ||||||||||||||||||||| |||  | ||||| || || ||||| || |||||||| ||| ||||||||||||||||||| ||||||| ||||| || || |   ||||  |      | ||||||  || || || |    || || |   ||  |||||| || |||||  ||||   |   ||||| | |       
GTCATGGAGGATCACGTGCTGCTGAGTATTTGAGGGAGCACTTGTTTGATAACCTTCTCAAGCACCCTGATTTCTTGACAGATACAAAGCTTGCGATAAgtattttttttccttcagctttactgta--gactttctgtt-gccattcttgttggtgtcgcaac--atgtttatctgctaaactt--gaaatttattacaaaaaacag------
















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|218504110|gb|FG960416.1|FG960416
EST:     AATCTTCTGGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAA                         GTGAAACATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATG
genomic: AATCTTCT-GAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttc ... ataacaacagGTGAAACATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATG
EST: gi|701451|gb|D47742.1|D47742
EST:     AAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAA                         GTGAA-CATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATG
genomic: AAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttc ... ataacaacagGTGAAACATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATG
EST: gi|38477230|gb|CF961363.1|CF961363
EST:     AAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAA                         GTGAAACATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATG
genomic: AAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttc ... ataacaacagGTGAAACATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATG

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: 72 (upstream exon), 74 (downstream exon)
Score: 22

GTCATGGAGGACCACGTGCTGCTGAGTATTTGAAGGAAAATTTGTTCGAAAATCTTCTGAAACACCCTGAGTTCCTGACAGATACAAAGCTTGCCATAAgtaatttttc ... ataacaacagGTGAAACATATCAGAAAACAGATACAGATTTCTTAGAATCAGAATCCAATGCCTTCAGGGATGATGGTTCAACAGCTTCCACTGCAGTTTTGGTGGGTGG




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