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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGATGCTGAAATTCTTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatgagcaattgattttgaaatctgtgactatgctgatcattattttattttactttatttttctacacattcatgtaatgttacactgtcatgaatgaacttttgaatgggttatttccaatctgtatgttctgtag

Basic information

species Zea mays
transcript GRMZM5G887631_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 19
GTCGGATGCTGAAATTCTTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatgagcaattgattttgaaatctgtgactatgctgatcattattttattttacttt---atttttctacacattcatgtaatgttacactgtcatgaatgaacttttgaatgggttatttccaatctgtatgttctgtag
 |||||||| || |||||||| ||||| || || |||||||| |||||||||||||||||||| |||||||    |||    ||| ||   | || | ||  | ||  |  | ||     |    |       |  |    ||  |||| |||  |  |    |    ||                                            
ATCGGATGCAGATATTCTTGGTCCTCATAGCCAATATCTTCCAAAAATTGTTTCAATTTTTGCGGAGgtaatttctgac---ttgtttcctatat-tatgg-tgtggggcccttttcccaaaggaaaacagagacatcaagacggattcctgtgttcctggtttagtttggt------------------------------------------
















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|211018174|gb|FL213619.1|FL213619
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|37377906|gb|CF625599.1|CF625599
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|60352763|gb|DN219736.1|DN219736
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|211015404|gb|FL213618.1|FL213618
EST:     TGGGCCTCACAGTCAGTATCTTCCTAAAATKCGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TGGGCCTCACAGTCAGTATCTTCCTAAAATT-GTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|32938382|gb|CF043201.1|CF043201
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|61119517|gb|DN560478.1|DN560478
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|5018426|gb|AI714619.1|AI714619
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|211333185|gb|FL444751.1|FL444751
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|4775831|gb|AI664836.1|AI664836
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|9028748|gb|BE238788.1|BE238788
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|9028539|gb|BE238534.1|BE238534
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGCTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|71770781|gb|DR968718.1|DR968718
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|211053072|gb|FL461740.1|FL461740
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCMCTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|60396898|gb|DN229717.1|DN229717
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|87155546|gb|DY400335.1|DY400335
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|26559254|gb|CA831489.1|CA831489
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|211015403|gb|FL213617.1|FL213617
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|7844583|gb|AW787805.1|AW787805
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|37396319|gb|CF635448.1|CF635448
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|60401162|gb|DN233969.1|DN233969
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|32930903|gb|CF035715.1|CF035715
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|9953899|gb|BE640482.1|BE640482
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|37382036|gb|CF627936.1|CF627936
EST:     TTGGTCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|8103149|gb|AW927807.1|AW927807
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
EST: gi|13149409|gb|BG319731.1|BG319731
EST:     TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAG                         GTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG
genomic: TTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATG

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: 46 (upstream exon), 49 (downstream exon)
Score: 102

GTCGGATGCTGAAATTCTTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATGGTGAATGTCTTGAGGCGTTTCCAGCAGACTTTGCCTCCTGATTTTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTCGGATGCTGAAATTCTTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATGGTGAATGTCTTGAGGCGTTTCCAGCAGACTTTGCCTCCTGATTTTCTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 71

GTCGGATGCTGAAATTCTTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATGGTGAATGTCTTGAGGCGTTTCCAGCAGACTTTGCCTCCTGATTTTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

GTCGGATGCTGAAATTCTTGGGCCTCACAGTCAGTATCTTCCTAAAATTGTTTCAATTTTTGCAGAGgtaagcaatg ... tgttctgtagGTTTTGTGCAATGGAACAGAACTTGCCACTGATGAAACTAGAAACAGGATGGTGAATGTCTTGAGGCGTTTCCAGCAGACTTTGCCTCCTGATTTTCTTG