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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTCTCCGCTAGGGCGCTCGGCTTCTCGCTTCGTCTCAAGCCGTCGCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgtttcatactggaattttttgctctctgtgcagcttcgtgtttgatttgttcctcagctgtgcccagcacttcatatttcatatttgttcttctttacggtagctatttcgactgactgtatttattccaagcacatttttttaatgattgcgttcaaaatcttcag

Basic information

species Zea mays
transcript GRMZM2G094255_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|31355338|gb|CD439695.1|CD439695
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006666|gb|FL081503.1|FL081503
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|71309481|gb|DR791027.1|DR791027
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGG--                         -ATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|78107718|gb|DV526136.1|DV526136
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006668|gb|FL081505.1|FL081505
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGG--                         -ATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006670|gb|FL081507.1|FL081507
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGG--                         -ATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|76289085|gb|DV028653.1|DV028653
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|76010863|gb|DT938033.1|DT938033
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006664|gb|FL081501.1|FL081501
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006671|gb|FL081508.1|FL081508
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|50325237|gb|CO520363.1|CO520363
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006662|gb|FL081499.1|FL081499
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|94478729|gb|EB707687.1|EB707687
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|76293135|gb|DV032703.1|DV032703
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006669|gb|FL081506.1|FL081506
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|74232836|gb|DT640750.1|DT640750
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|76284484|gb|DV024052.1|DV024052
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|88757021|gb|DY541162.1|DY541162
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|91056439|gb|EB166857.1|EB166857
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGG--                         -ATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|31611949|gb|CD568571.1|CD568571
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211003886|gb|FL081493.1|FL081493
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|149110134|gb|EE293952.2|EE293952
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|101397352|gb|EB820599.1|EB820599
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006657|gb|FL081494.1|FL081494
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|78112492|gb|DV530886.1|DV530886
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---G                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: TGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC

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), 47 (downstream exon)
Score: 69

GCTTTCTCCGCTAGGGCGCTCGGCTTCTCGCTTCGTCTCAAGCCGTCGCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 74

GCTTTCTCCGCTAGGGCGCTCGGCTTCTCGCTTCGTCTCAAGCCGTCGCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 77

GCTTTCTCCGCTAGGGCGCTCGGCTTCTCGCTTCGTCTCAAGCCGTCGCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 40

GCTTTCTCCGCTAGGGCGCTCGGCTTCTCGCTTCGTCTCAAGCCGTCGCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgt ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTCTCCGCTAGGGCGCTCGGCTTCTCGCTTCGTCTCAAGCCGTCGCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTGgttcgtgtgtttcatactggaattttttgctctctgtgcagcttcgtgtttgatttgttcctcagctgtgcccagcacttcatatttcatatttgttcttctttacggtagctatttcgactgactgtatttattccaagcacatttttttaatgattgcgttcaaaatcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA