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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGAAATAGCAGACTCATGGGAATTATGGAATTCATTCAGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtcatacctgcccataccagtacttttgcaactatttaattattcttaatctataatgcaatagctttggtattcaaaaagatgcattcttttaccag

Basic information

species Zea mays
transcript GRMZM2G011456_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 5'ss of exon 5
AGTGAAATAGCAGACTCATGGGAATTATGGAATTCATTCAGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtcatacctgc----ccatacca-gtactt--ttgcaactat-----ttaattattcttaatctataatgcaatagctttggtattca----aaaagatg--cattcttttaccag
||||| |  | |||||| |||||||  ||||||||||| ||| |  ||||||| ||||| || ||||| || ||||| |||||| ||| |||||||   | | |||        |||| || |||  || ||| |       | | | ||  | ||||||| |||  |||| |||||| ||||    ||| | ||   ||||  ||| |||
AGTGATACCGTAGACTCTTGGGAATGGTGGAATTCATTTAGACTATTATGTGAGCATAGCAGTCAACTGTGTGTGGCGCTTGATGTTTTgtaagtgatgttcttgcattgttgcaccaagtgctttcttccaagtgaagatgtcactgataataaatctatcatgttatagttttggttttcattacaaaggttggctattcacttatcag
















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|211230912|gb|FL222481.1|FL222481
EST:     AGAT-GCTATGTGACCATAGTAGCCCACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTTAAGGCGCTGGTTTGGGGAGCCTG
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATT-AGGGCGCTGGTTTGGGGAGCCTG
EST: gi|71311078|gb|DR791853.1|DR791853
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
EST: gi|71300983|gb|DR786520.1|DR786520
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
EST: gi|89762829|gb|DY690269.1|DY690269
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATT
EST: gi|91876145|gb|EB406102.1|EB406102
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAAC
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAAC
EST: gi|74233408|gb|DT641322.1|DT641322
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT
EST: gi|78117239|gb|DV535626.1|DV535626
EST:     AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTC                         GGGCACACTGCCATCAATGAACTCATTANGGCGCTGGTTTGGGGAGCCTGT
genomic: AGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGT

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: 544

AGTGAAATAGCAGACTCATGGGAATTATGGAATTCATTCAGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

AGTGAAATAGCAGACTCATGGGAATTATGGAATTCATTCAGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

AGTGAAATAGCAGACTCATGGGAATTATGGAATTCATTCAGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 323

AGTGAAATAGCAGACTCATGGGAATTATGGAATTCATTCAGATTGCTATGTGACCATAGTAGCCAACTATGCGTGGCACTTGATATTTCgtaagtgtca ... cttttaccagGGGCACACTGCCATCAATGAACTCATTAGGGCGCTGGTTTGGGGAGCCTGTAAGGGCTGCTATTCTGCAAACCAAT