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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcattttttgttgttgtaaacgatgcatgctatatttgatatggaattcttgctctgcaatgttaacctgttgccaagtaaatttaccaatacgatagtgtaataactttttattgattcatgtgatcatgcattgatgaatcacttacatttgccctacttcttgcag

Basic information

species Zea mays
transcript GRMZM2G160842_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160842_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 5'ss of exon 6
ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcattttttgttgttgtaaacgatgcatgctatatttgatatggaattcttgctctgcaatgttaacctgttgccaagtaaatttaccaatacgatagtgtaataactttttattgattcatgtgatcatgcattgatgaatcacttacatttgccctacttcttgcag
||||||||||||||| ||||| || ||||| ||||||||| | || |||||||| || || ||||| |||||||| ||||||| ||| |  ||    |  |||||  |||||  | ||| || | |||   ||| | |   | |||   ||  |    |  || |  |     | |  | |   |                                                                     
ATATGATATAGTTGTAGATGCCACGGACAATCTTCCTACTCGATACATGATCAGTGACTGTTGTGTGTTGCTGAATAAGgtaaattcttgcttc--cgaggtaaataatgcagtcaatacttcaaatg---ttcat-caggggaataccaattttcatcttagcatgtaatttagtgagtttcag---------------------------------------------------------------------

upper sequence: GRMZM2G160842_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g56080.1 (Oryza sativa), 5'ss of exon 5
ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgta---acttcattttttgttgttgtaaacgatgcatgctatatttgatatggaattcttgctctgcaatgttaacctgttgccaagtaaatttaccaatacgatagtgtaataactttttattgattcatgtgatcatgcattgatgaatcacttacatttgccctacttcttgcag
|||||| ||||| ||||| |||||  ||||||| |||| | |||| |||||||| ||||| |||||  || |||||||||||   | ||||  |||  || |  | | |  ||  ||  ||| |  ||||        ||    | |  ||    ||  |  |  | | | |   ||   |                                                                            
ATATGACATAGTAGTTGACGCAACAAACAACCTGCCTAGTCGGTACATGATCAGTGATTGTTGTGTCCTGATGAACAAGgtataaagttcagctttgtttctcatcatctctgtttgtaatagtacatataag----ctgtgacggagcgtggggctcctcaccgggagactgcgcaggcccc--------------------------------------------------------------------------
















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|211086842|gb|FL241958.1|FL241958
EST:     ACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG                         CCACTTGTATCTGGTGCGGCATTAGGCTTANAAGGGCAG
genomic: ACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG
EST: gi|16746025|gb|BM032455.1|BM032455
EST:     GTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG                         CCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG
genomic: GTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG
EST: gi|148954835|gb|EC900308.2|EC900308
EST:     ACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG                         CCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG
genomic: ACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG
EST: gi|18384856|gb|BM418055.1|BM418055
EST:     GTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG                         CCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG
genomic: GTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 179

ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 140

ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAGgtaacttcat ... cttcttgcagCCACTTGTATCTGGTGCGGCATTAGGCTTAGAAGGGCAG