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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggacttaggacgcgtgctagctgttcttggctctggcatttctcggaggctttgatttgatctgggcactgtttggttgttcag

Basic information

species Zea mays
transcript GRMZM2G138886_T01
intron # 4
splice site 5'
intron type U2

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|211247234|gb|FL156674.1|FL156674
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAAGGGCCAACCTGAATGTCAGCCGA
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAA-GGGCCAACCTGAATGTCAGCCGA
EST: gi|211249461|gb|FL156681.1|FL156681
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211249469|gb|FL156689.1|FL156689
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|148972285|gb|EE023184.2|EE023184
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211249468|gb|FL156688.1|FL156688
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|76283026|gb|DV022594.1|DV022594
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211249467|gb|FL156687.1|FL156687
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|50324450|gb|CO519576.1|CO519576
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|76294034|gb|DV033602.1|DV033602
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211249466|gb|FL156686.1|FL156686
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211004196|gb|FK981412.1|FK981412
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211004197|gb|FK981413.1|FK981413
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATG
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATG
EST: gi|71439376|gb|DR820426.1|DR820426
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|30307157|gb|CD001830.1|CD001830
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|149081651|gb|EE170801.2|EE170801
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211249460|gb|FL156680.1|FL156680
EST:     AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
EST: gi|211249462|gb|FL156682.1|FL156682
EST:     AGAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAG                         GAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT
genomic: AAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGAT

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

GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGATCGTAGCTGATCCAGAACCCGAAGTTTGTCAACAGAAGGAATCAGTAGGC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 8

GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGATCGTAGCTGATCCAGAACCCGAAGTTTGTCAACAGAAGGAATCAGTAGGC


Block sizes: 40 (upstream exon), 43 (downstream exon)
Score: 13

GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGATCGTAGCTGATCCAGAACCCGAAGTTTGTCAACAGAAGGAATCAGTAGGC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 21

GAAGAGCAAAAGGGACGAAAAGCAGCCAGCGTTGGCAAGCAGCCGGCCCATGACAAGgttaggactt ... ggttgttcagGAAATTCGCCGCCTCCTTGGCGAGCAAGGGCCAACCTGAATGTCAGCCGATCGTAGCTGATCCAGAACCCGAAGTTTGTCAACAGAAGGAATCAGTAGGC