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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataatccaggaatttcttatagagatttgtagggtgtttcatttttttgtaagtattgtcagttgttaaagtaaattaaaatgcttttcttaactcaattgatttgttcccatttatcatttcattgtatttttgcag

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 6
AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataatccaggaatttcttatagagatttgtagggtgtttcatttttttgtaagtattgtcagttgttaaagtaaattaaaatgcttttcttaactcaattgatttgttcccatttatcatttcattgtatttttgcag
||||||||||| |||||||| ||||  |||||||||||||||||||| |||||||| |||||||||||||||| ||| | ||    ||||| |  ||   || | |      ||| || ||| |  ||| | | | || |||       |||     | | || |   | |||  |  |    |                            
AAAGAAGTTGCACAATTCACCTGTCAATCTGAGCGCCACATTGGAACACAATCTGGGGGCATGGATCAGgtaa-atagttcatagttttctaactga---ttatggtaatactcagttcttttt--gtactttaacttatta-------ttatgccacctgtcatg--taaatcaaagtacatc----------------------------
















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|76290432|gb|DV030000.1|DV030000
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|50330093|gb|CO525219.1|CO525219
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|32806294|gb|CD958528.1|CD958528
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTA
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTA
EST: gi|76283981|gb|DV023549.1|DV023549
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATC
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATC
EST: gi|148955644|gb|EC901316.2|EC901316
EST:     TTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGGCGGCATGGATCAG                         GGTATATCTATCATGGCGAAAC-TGAATTCGCTG
genomic: TTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGG-CGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTG
EST: gi|148972046|gb|EE022887.2|EE022887
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|17921536|gb|BM259187.1|BM259187
EST:     TGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: TGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|149071533|gb|EE159924.2|EE159924
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|76912626|gb|DV164825.1|DV164825
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|148965140|gb|EE015956.2|EE015956
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGC
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGC
EST: gi|78085244|gb|DV513637.1|DV513637
EST:     TTGTCTGTCTGAGCGCCACATTGGAACGNCA-TCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTT
genomic: TTGTCTGTCTGAGCGCCACATTGGAACG-CAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTT
EST: gi|148991238|gb|EE032704.2|EE032704
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|17921866|gb|BM259517.1|BM259517
EST:     TTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGTATTCGCTGAGTTGATAGATTTTAAT
genomic: TTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|148951727|gb|EC897480.2|EC897480
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|71318360|gb|DR795942.1|DR795942
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTTAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|148967123|gb|EE018297.2|EE018297
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|211139371|gb|FL028742.1|FL028742
EST:     CTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
EST: gi|108824283|gb|EC278291.1|EC278291
EST:     CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAG                         GCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT
genomic: CTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAAT

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), 44 (downstream exon)
Score: 86

AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAATCCAATCCATGCAACTGACGTCCAACTACCTTCAGGTGGTACATTTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 226

AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAATCCAATCCATGCAACTGACGTCCAACTACCTTCAGGTGGTACATTTGTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 234

AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAATCCAATCCATGCAACTGACGTCCAACTACCTTCAGGTGGTACATTTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataat ... atttttgcagGCTATATCTATCATGGCGAAACCTGGATTCGCTGAGTTGATAGATTTTAATCCAATCCATGCAACTGACGTCCAACTACCTTCAGGTGGTACATTTGTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAAGTTGCTCAATTCACTTGTCTGTCTGAGCGCCACATTGGAACGCAATCTGGCGGCATGGATCAGgtaatataatccaggaatttcttatagagatttgtagggtgtttcatttttttgtaagtattgtcagttgttaaagtaaattaaaatgcttttcttaactcaattgatttgttcccatttatcatttcattgtatttttgcag

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