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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaacttgttaagttgttagagcatattgttcatttgttctgttttgcagacataacttccacatgtacttgtgatgaactgcttgctaactattg...

Basic information

species Zea mays
transcript GRMZM2G136389_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136389_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g07990.1 (Oryza sativa), 5'ss of exon 2
CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaacttgttaagttgttagagcatattgttcatttgttctgttttgcagacataacttccacatgtacttgtgatgaactgcttgctaactattg----
||||||||||||||||||| |||| |||||||||||||||||||||||||| |||||||||||||||||||| |||||| | || ||||||||||||||||||     ||||| |  |    | | ||| | | |  ||   ||||      | |||  ||| | |  |   ||    ||   |||       | | | |    
CAATCGTCTTCGACCCTCAGTTGAGGAAAGTGATTGCAAATACAAAAGATTTTTTGGCTGCTATGTTGCTCGGGAGGCTATAATTGATGAGGAATACTGGgtatatttcttgtcacctgtagaaaacat-tagattgttaactctggg--aaatacactactacaattttcgctgac-atagcctgtacaggtattttggagta
















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|89247752|gb|DY619538.1|DY619538
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|78114509|gb|DV532898.1|DV532898
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|71319331|gb|DR796417.1|DR796417
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|76291396|gb|DV030964.1|DV030964
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|15100324|gb|BI396115.1|BI396115
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTAATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|89758710|gb|DY687791.1|DY687791
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|50323554|gb|CO518680.1|CO518680
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|71431214|gb|DR812264.1|DR812264
EST:     GGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: GGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|18963822|gb|BM660649.1|BM660649
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTAATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|71431215|gb|DR812265.1|DR812265
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|101382964|gb|EB813535.1|EB813535
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|91878484|gb|EB408441.1|EB408441
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTAATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|91876453|gb|EB406410.1|EB406410
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|94472235|gb|EB701193.1|EB701193
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|87153075|gb|DY397864.1|DY397864
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTAATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|71429124|gb|DR810174.1|DR810174
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|71307824|gb|DR790133.1|DR790133
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|78114508|gb|DV532897.1|DV532897
EST:     TATTTGGCTGTTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
EST: gi|149009815|gb|EE041700.2|EE041700
EST:     TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGG                         ATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT
genomic: TATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAAT

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), 47 (downstream exon)
Score: 46

CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 70

CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaact ... tgattgatagATCGCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCGTCTTCGACCCTCAATTGATGAAAGTGATTGCAAATACAAAAGATTATTTGGCTGCTATGTTGCTCGTGAGGCTGTGATCGATGAGGAATACTGGgtaataaacttgttaagttgttagagcatattgttcatttgttctgttttgcagacataacttccacatgtacttgtgatgaactgcttgctaactattg

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