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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtttgcacattctctttctactatatagaataagtgctattgttggaccaatcgcgaccaaggccctgttttcttgaacttgatctcatcagtatttattcttatcacag

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 8
GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtttgcacattctctttctactatatagaataagt---gctattg----ttggaccaatcgcgaccaaggccctgttttcttgaactt--gatctcatcagtatttattcttatcacag
||||| ||||||||||||| |||||||||||| || ||||||||||||||   | ||| | || |  || |||||     ||| |||   |||| ||    | || ||| |   | ||| |    | || |||  | |||  ||||| |||||||   || ||||   |||
GATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAGgttag---tgtgcccgttgtggttgtactaatcccaatgagtatggctactgccaatcggtccattgctgtccaggcttattttatctgtagcttatgatctgatcagtagaaat-cttaatgcag
















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|76293424|gb|DV032992.1|DV032992
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|9953883|gb|BE640466.1|BE640466
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|76293423|gb|DV032991.1|DV032991
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|78117581|gb|DV535968.1|DV535968
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|149100778|gb|EE186872.2|EE186872
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|9028732|gb|BE238772.1|BE238772
EST:     TTCAGGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: TTCAGGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|60339232|gb|DN206205.1|DN206205
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|60359240|gb|DN226213.1|DN226213
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|60355012|gb|DN221985.1|DN221985
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|148951737|gb|EC897492.2|EC897492
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|60341646|gb|DN208619.1|DN208619
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|148964885|gb|EE015747.2|EE015747
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|71310909|gb|DR791757.1|DR791757
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|101397216|gb|EB820532.1|EB820532
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
EST: gi|60353036|gb|DN220009.1|DN220009
EST:     GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG                         ATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT
genomic: GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 106

GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGgttagatgtt ... cttatcacagATCGGAACTGACATTGAAGACTACAAATGTTCCTGGCTAGTTGTGCAAGCTCTTGAGCGTGCTGCTGAGAACCAAAAGAGCATTCTGTTT