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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctatattgtgttctctgttgatgtgtgattcgatcaatctttagtcttaaaattctgaaacttccttgtgatgatcttattggtgtggaacaat...

Basic information

species Zea mays
transcript GRMZM2G158162_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158162_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g48200.2 (Oryza sativa), 5'ss of exon 10
GGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctatat-tgtgttctctgttgatgtgtgattcgatcaatctttagtcttaaa-attctgaaacttccttgtgatgatcttattggtgtggaaca-at------
||||||||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| ||||||||  | |||||| ||   ||| ||||| |||| |||| | | ||      |  |  |       ||   ||| |   |||   |    ||| |  | | |  ||  | | |    | |  | |  |||| ||      
GGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTTACCACTTAATGTTATTGTTGCATCCAAGTGGACATGTGCTGACAACACAATCGACTCAAAAAGgta-tgctgtttgtggaaaaacattctagccacactttcgtcatttgatagaactgttcattgtacatcatgatta-gctaactaaaattatttccaacatatttgcag
















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|148956308|gb|EC902110.2|EC902110
EST:     ATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATG                         CTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGT
genomic: ATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGT
EST: gi|60397624|gb|DN230440.1|DN230440
EST:     ATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATG                         CTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGT
genomic: ATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGT
EST: gi|67034443|gb|CO462993.1|CO462993
EST:     AT-GNTGCATCCAAATGGACATGCGCCGACAACTCATGGGACCCAAA-TG                         CTGCTCCTGCTCTGCGCCTG
genomic: ATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTG

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 171

GGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 200

GGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

GGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 518

GGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCATGGGACCCAAAATGgtaatgctat ... actgtttcagCTGCTCCTGCTCTGCGCCTGAAGAGTTGACCCCAAAAGAGTTGCAAAGTGTTATGCAGCAGTATGAAG