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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCATCCTGGAGGTTTTCTTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttctttatcttacttttttattcttcttgaaatttttatatgtacatacatgattaaatttggtaatctcgtgaaccatgatattgatgttatgttcctgatttgcattattttaatttaatatgattttaaaaatgcag

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 15
GCGCATCCTGGAGGTTTTCTTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttctttatcttacttttttattcttcttgaaatttttatatgtacatacatgattaaatttggtaatctcgtgaaccatgatattgatgttatgttcctgatttgcattattttaatttaatatgattttaaaaatgcag
|| || || || || |||||||| ||||||||||| |||||||||||||| || ||||||||||||||||||||  || |   |||||     ||  ||    ||   ||| |||  || | ||      |||||   | | | |    | ||||| |  |||| | |  |  |||||  ||||| || || | ||| |||               
GCCCACCCAGGTGGATTTCTTTTTACAAAGTTTGCTAGTAGCAGCCAGACGCTATTTGACCTTTTCCCGgtaacaattttcattctta-----ttggtcacaatgttctttctatcagtgctta------taaat---gcactatatgaacccatggttctgatataac-tatctgat--gcattgttata-tctaaaatgcag------------
















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|211048835|gb|FL187595.1|FL187595
EST:     GACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
genomic: GACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
EST: gi|6994163|gb|AW453377.1|AW453377
EST:     TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
genomic: TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
EST: gi|211048840|gb|FL187600.1|FL187600
EST:     TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTG
genomic: TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTG
EST: gi|67034427|gb|CO462977.1|CO462977
EST:     TGACCTTTTCTCC-                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAA
genomic: TGACCTTTTC-CCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAA
EST: gi|211051787|gb|FL187605.1|FL187605
EST:     GACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
genomic: GACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
EST: gi|211051789|gb|FL187607.1|FL187607
EST:     TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCG                         GATAGCTTTGGTAGC
genomic: TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGC
EST: gi|211051788|gb|FL187606.1|FL187606
EST:     GACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
genomic: GACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
EST: gi|211048839|gb|FL187599.1|FL187599
EST:     GACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
genomic: GACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
EST: gi|32801048|gb|CD953284.1|CD953284
EST:     TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCG                         GATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG
genomic: TTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAG

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), 47 (downstream exon)
Score: 173

GCGCATCCTGGAGGTTTTCTTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAGGCAATGAAACATCTGAATAAGCTTTTCCCAAACAAGATTTCGATTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GCGCATCCTGGAGGTTTTCTTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAGGCAATGAAACATCTGAATAAGCTTTTCCCAAACAAGATTTCGATTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

GCGCATCCTGGAGGTTTTCTTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAGGCAATGAAACATCTGAATAAGCTTTTCCCAAACAAGATTTCGATTCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GCGCATCCTGGAGGTTTTCTTTTCACAAAGTTTGCCAGTAGCAGCCAGACACTTTTTGACCTTTTCCCGgtaacttttc ... aaaaatgcagGATAGCTTTGGTAGCAGGTGGTTGCATGAAAGAAGCAAAGAAAGTCCAAAGGCAATGAAACATCTGAATAAGCTTTTCCCAAACAAGATTTCGATTCAGC