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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaacaaatgatattagaaattcaatttttctattgaaatatacatcacatcaatatttatttaggtgtcattttgtcag

Basic information

species Zea mays
transcript GRMZM2G315931_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 5'ss of exon 10
GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaacaaatgatattagaaattcaatttttctattgaaatatacatcacatcaatatttatttaggtgtcattttgtcag
||||||||||| || ||||| |||||||| ||||| ||||||||||| |||||| | |||||  ||||| |            || |     | || | |   |||| ||| |||||| | | | || ||  |||
GTAATTGCTTGCCCATGTGCCCTTGGGCTCGCCACACCCACTGCTGTGCTGgtatgcaacaa--gatatga----------ccttttgcctgagtaaatagtccatccataattatttggatat-atgtttccag

upper sequence: GRMZM2G315931_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S121_53V6.1 (Physcomitrella patens), 5'ss of exon 11
GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaacaaatgatattagaaattc----aatttttctat--tgaaatat--acatcacatcaatatttatttaggtgtcattttgtcag---------
|| |||||||| |||||||||||||| ||||| ||||| || ||||| |||||| | ||| | |   | ||   ||      | | | |  ||  |||| | |  |      | |||  ||  |||   |   ||| |  | |         
GTCATTGCTTGCCCTTGTGCTCTTGGACTTGCGACTCCTACAGCTGTTCTGgtatgcaactagtaggaatatggatgtgtagagtctgttgatgctgaagtgttgaagctctagcaaggtt-gtttgtattaaattatacctggatcttagt
















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|211170366|gb|FL103275.1|FL103275
EST:     CTTGGGCTTGCCACTCCCACTGCTGTACTG                         GTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGAT
genomic: CTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGAT
EST: gi|211050287|gb|FL014623.1|FL014623
EST:     ATTGCTTGTCCTTGTGCNNTCT-GG-CTTGCCACTCCCACTGCTGTACTG                         GNTGGCANCTTCATTAGGTGCAACAGGAAGACCTCTTTTACGT
genomic: ATTGCTTGTCCTTGTGC--TCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCA-CTTCATTAGGTGCAACAAGAGGACTTCTTTTACGT
EST: gi|13125965|gb|BG316640.1|BG316640
EST:     CTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTG                         GTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGAT
genomic: CTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGAT
EST: gi|211050286|gb|FL014622.1|FL014622
EST:     TAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTG                         GTTGGCACTTCATTAGGTGCAACAAGAAGACTTCTTT-ACGTGGTGGGGAT
genomic: TAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGAT

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: 149

GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGATGTTTTGGAGAAGTTCTCTGATGTTGATGCCGTTGTGTTTGACAAGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGATGTTTTGGAGAAGTTCTCTGATGTTGATGCCGTTGTGTTTGACAAGACTG


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

GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGATGTTTTGGAGAAGTTCTCTGATGTTGATGCCGTTGTGTTTGACAAGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

GTAATTGCTTGTCCTTGTGCTCTTGGGCTTGCCACTCCCACTGCTGTACTGgtaggaaaca ... attttgtcagGTTGGCACTTCATTAGGTGCAACAAGAGGACTTCTTTTACGTGGTGGGGATGTTTTGGAGAAGTTCTCTGATGTTGATGCCGTTGTGTTTGACAAGACTG