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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTTACAGTACATGCGACTCAGAAGTATTTTGTGAGTGCTTCCAAGGATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctccatcagacattcacacattttcttactacacataagtatgcaactatgcattccaatgtgtatgattgttttgatcag

Basic information

species Zea mays
transcript GRMZM2G037698_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037698_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 10
AGCTGTTACAGTACATGCGACTCAGAAGTATTTTGTGAGTGCTTCCAAGGATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctccatcagacattcacacattttcttactacacataagtatgcaactatgcattccaatgtgtatgattgttttgatcag-----------------------------------
|||||||||||| ||||||||||||||||| ||||||| |||||||||||||||| | ||||||||||| |||||| || ||||||||||||| |||||||||  |||||| |  | ||| ||  |   ||     ||   |   ||| |  ||| ||| |   | ||| || | | |   |  |                                    
AGCTGTTACAGTCCATGCGACTCAGAAGTACTTTGTGACTGCTTCCAAGGATAATACTTGGTGCTTCTACGATATTCCATCAGGATCTTGCCTCACACAGgtttactccattat-ctttctcatgtaacctgctcccattcatccatgtacttatacatgc---tttgtctgttagctcccaagatgtttatgagttaatgaataccttttctttactcag
















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|211125233|gb|FL005606.1|FL005606
EST:     ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAG                         GTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
genomic: ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
EST: gi|32908360|gb|CF013173.1|CF013173
EST:     ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAG                         GTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
genomic: ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
EST: gi|32934237|gb|CF039049.1|CF039049
EST:     ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAG                         GTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCACCCA
genomic: ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
EST: gi|32933281|gb|CF038093.1|CF038093
EST:     ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAG                         GTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
genomic: ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
EST: gi|32837457|gb|CD977135.1|CD977135
EST:     ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAG                         GTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
genomic: ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
EST: gi|33103734|gb|CF063694.1|CF063694
EST:     ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAG                         GTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA
genomic: ATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCA

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), 48 (downstream exon)
Score: 193

AGCTGTTACAGTACATGCGACTCAGAAGTATTTTGTGAGTGCTTCCAAGGATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 77

AGCTGTTACAGTACATGCGACTCAGAAGTATTTTGTGAGTGCTTCCAAGGATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 94

AGCTGTTACAGTACATGCGACTCAGAAGTATTTTGTGAGTGCTTCCAAGGATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTT


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 71

AGCTGTTACAGTACATGCGACTCAGAAGTATTTTGTGAGTGCTTCCAAGGATAATTCGTGGTGCTTCTATGATATTTCAACAGGATCTTGCCTGACACAGgttacctcca ... ttttgatcagGTTGGCGAGGCTTCAGGACAAGAGGGATATACATCCGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTT