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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgtttcctgtttacagcaacttgcatgcctgtgcttgagattgatgatcatatgaccgcaatgacaaatctagagtaaaattcagggatgggg...

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 12
CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgtttcctgtttacagcaacttgcatgcctgtg-cttgagattgatgatcatatgaccgcaatgacaaatctagagtaaaattcagggatgggg-
 |||||||||| |||||||| ||||| || ||||||||||||||||| ||||| || || | | |||| ||||| |||||||||||||||||  | |  ||   |  ||   ||    |   ||  ||   |||   ||||      |  |        || |   |   |  | | |||   |  |     
TTGAAGCCTGGTGGTGAAATCCCAGCCAAAGGAAAGAAAATTACACTACGTGTGCAGAACGGAAAAGATCTTACACGTGATGTCATAAAGgtcagaaatttgttttcttg--gcggtgttgttgtttgcaactttgcattgcatgcaacttttttagtgtgcctgcttgtgcatgagatttctgacttatct
















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|60348538|gb|DN215511.1|DN215511
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|6445448|gb|AW179366.1|AW179366
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|20513026|gb|BQ280212.1|BQ280212
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|78544301|gb|DV621799.1|DV621799
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|211367141|gb|FL432366.1|FL432366
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|211282780|gb|FL192971.1|FL192971
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|88748313|gb|DY532454.1|DY532454
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|20803326|gb|BQ294376.1|BQ294376
EST:     ATGCCCAAGCCCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTCCCTGAACTTGAGTTGGAACTTTCATGT
genomic: ATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|30306974|gb|CD001647.1|CD001647
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|78085694|gb|DV514087.1|DV514087
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|31611962|gb|CD568584.1|CD568584
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|29945539|gb|CB815690.1|CB815690
EST:     TTACNCTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|211282779|gb|FL192970.1|FL192970
EST:     CACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: CACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|37401209|gb|CF637968.1|CF637968
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|67020485|gb|CO449234.1|CO449234
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|60353658|gb|DN220631.1|DN220631
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|60395671|gb|DN228541.1|DN228541
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|29946582|gb|CB816222.1|CB816222
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|211282782|gb|FL192973.1|FL192973
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|78543505|gb|DV621003.1|DV621003
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|149027381|gb|EE046513.2|EE046513
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|78543967|gb|DV621465.1|DV621465
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|60350354|gb|DN217327.1|DN217327
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|113655504|gb|DW808848.1|DW808848
EST:     GTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAA-GTACCTGAACTTGAGTTGGAACTT
genomic: GTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTT
EST: gi|28568977|gb|CB280852.1|CB280852
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|7135394|gb|AW498064.1|AW498064
EST:     TACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|211367140|gb|FL432365.1|FL432365
EST:     TTACMCTGSGTGTTCAAAATGCMCAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|7135020|gb|AW497876.1|AW497876
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|60357973|gb|DN224946.1|DN224946
EST:     TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: TTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
EST: gi|211282781|gb|FL192972.1|FL192972
EST:     AAAATGCACAAGACCTTACTCGTGATGKCATAAAG                         TCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT
genomic: AAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGT

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), 41 (downstream exon)
Score: 279

CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGTGGAACGTTGGGTGGTATGGTCACAACTGTTGAAGGTTTAATTGTGAAAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 164

CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGTGGAACGTTGGGTGGTATGGTCACAACTGTTGAAGGTTTAATTGTGAAAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 116

CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGTGGAACGTTGGGTGGTATGGTCACAACTGTTGAAGGTTTAATTGTGAAAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 124

CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgt ... tgtttttcagTCAGATTCAGCTAGCGTAAAAGTACCTGAACTTGAGTTGGAACTTTCATGTGGAACGTTGGGTGGTATGGTCACAACTGTTGAAGGTTTAATTGTGAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAGgtttggatgtttcctgtttacagcaacttgcatgcctgtgcttgagattgatgatcatatgaccgcaatgacaaatctagagtaaaattcagggatgggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagtaaaa