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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTCTTCCCCTCTCCACTCCCAATCTTATCGTCGCCTCCCTCGACGTCGCTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccccttcacgcctgcgcgctaggttcttgatttagaccgtttcctgtgttgtccgtgtcggaatctgctggtcccgtctttcgaacccaacga...

Basic information

species Zea mays
transcript GRMZM2G069765_T01
intron # 1
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|149105498|gb|EE291023.2|EE291023
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|60358233|gb|DN225206.1|DN225206
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229383|gb|FL136771.1|FL136771
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|149082543|gb|EE171738.2|EE171738
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229393|gb|FL136781.1|FL136781
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211227330|gb|FL136768.1|FL136768
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|33093832|gb|CF053826.1|CF053826
EST:     CTACTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|6021027|gb|AW065955.1|AW065955
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211231448|gb|FL136784.1|FL136784
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229384|gb|FL136772.1|FL136772
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229382|gb|FL136770.1|FL136770
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|78083040|gb|DV511433.1|DV511433
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211231449|gb|FL136785.1|FL136785
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|33097192|gb|CF057152.1|CF057152
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|76014861|gb|DT942031.1|DT942031
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229381|gb|FL136769.1|FL136769
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|22491088|gb|BU051011.1|BU051011
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229392|gb|FL136780.1|FL136780
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229385|gb|FL136773.1|FL136773
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|31357629|gb|CD441986.1|CD441986
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211231451|gb|FL136787.1|FL136787
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|32865501|gb|CF005183.1|CF005183
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|19351773|gb|BM896305.1|BM896305
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|32908744|gb|CF013557.1|CF013557
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229388|gb|FL136776.1|FL136776
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229394|gb|FL136782.1|FL136782
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229391|gb|FL136779.1|FL136779
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCAAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|87153647|gb|DY398436.1|DY398436
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|31354825|gb|CD439182.1|CD439182
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211229386|gb|FL136774.1|FL136774
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|31354522|gb|CD438879.1|CD438879
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|148949761|gb|EC895244.2|EC895244
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|31354218|gb|CD438575.1|CD438575
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|211231450|gb|FL136786.1|FL136786
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
EST: gi|149084479|gb|EE173941.2|EE173941
EST:     CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGA                         AGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC
genomic: CTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCC

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: 45 (upstream exon), 49 (downstream exon)
Score: 419

CCCTCTTCCCCTCTCCACTCCCAATCTTATCGTCGCCTCCCTCGACGTCGCTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 308

CCCTCTTCCCCTCTCCACTCCCAATCTTATCGTCGCCTCCCTCGACGTCGCTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 276

CCCTCTTCCCCTCTCCACTCCCAATCTTATCGTCGCCTCCCTCGACGTCGCTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 181

CCCTCTTCCCCTCTCCACTCCCAATCTTATCGTCGCCTCCCTCGACGTCGCTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccc ... gtctgaacagAGGACTCGCTGAAGCGGGAGTCTGGCGCGAAGGTTCACCAAGCCAACATCCAGGCGGCCAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTCTTCCCCTCTCCACTCCCAATCTTATCGTCGCCTCCCTCGACGTCGCTGCTGCCTCCACTTCACCATGGCGCTTCACGCCCCGGTCCTCGTTCTGAgtaagcgccccttcacgcctgcgcgctaggttcttgatttagaccgtttcctgtgttgtccgtgtcggaatctgctggtcccgtctttcgaacccaacga

- - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcccct