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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgactaacatacacccttctcttttcttttttaaccatcaagtagaattacgctattgtttatagagcacaaattgattccacaaatccatatactcgggtagcctccattaaagagaaggaacaataagcttctccagctcttccataatggactttaaaggaaccattttcttgtag

Basic information

species Zea mays
transcript GRMZM2G000718_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000718_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 5'ss of exon 6
AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgactaa--catacacccttctcttttcttttttaaccatcaagtagaattacg-ctattgtttatagagcacaaattgattccacaaatccatatactcgggtagcctccattaaagagaaggaacaataagcttctccagctcttccataatggactttaaaggaaccattttcttgtag
|||||||||||||| |||||||     ||||||||||||| ||||||||||| ||||||| ||||||||| || |||| ||||||| | ||     | |   | | ||||| |    || |  | ||| |   |  |      ||  || |||                                                                                                                  
AAATGTCAAATCAACAACTCATGGATGCCGGAAGGAAACAGATGGACCAAACAGATCAAGTTATTGAGCGTTCGAAAAAGgtgcgctagtagattttgctttcatttctttacacacttcaagagcaaattttacaagaatcctttcttgtag------------------------------------------------------------------------------------------------------------------
















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|148993115|gb|EE033715.2|EE033715
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|211130915|gb|FL136653.1|FL136653
EST:     CAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: CAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|6022470|gb|AW067503.1|AW067503
EST:     GAAGAAAACAAATGGATCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60354623|gb|DN221596.1|DN221596
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|149002889|gb|EE038886.2|EE038886
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60346808|gb|DN213781.1|DN213781
EST:     GCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAATTCTGACA
genomic: GCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|148941490|gb|EC886419.2|EC886419
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|21843414|gb|BQ703995.1|BQ703995
EST:     GAAGAAAACAAATGGATCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|37420501|gb|CF647941.1|CF647941
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60398834|gb|DN231650.1|DN231650
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|33466594|gb|CF243643.1|CF243643
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|71327359|gb|DR800293.1|DR800293
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60349330|gb|DN216303.1|DN216303
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|148993116|gb|EE033716.2|EE033716
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|50333643|gb|CO528769.1|CO528769
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60345394|gb|DN212367.1|DN212367
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|149112851|gb|EE295664.2|EE295664
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60352046|gb|DN219019.1|DN219019
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|149009782|gb|EE041679.2|EE041679
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|78117925|gb|DV536312.1|DV536312
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|149089650|gb|EE178904.2|EE178904
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|211386633|gb|FL468002.1|FL468002
EST:     TGAGCGCTCAAAAATG                         GTTGTAGCMCAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAAYTYTGACA
genomic: TGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|78083753|gb|DV512146.1|DV512146
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|91869534|gb|EB400432.1|EB400432
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|71327358|gb|DR800292.1|DR800292
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|30088413|gb|CB886618.1|CB886618
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60344730|gb|DN211703.1|DN211703
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|28361634|gb|CB239990.1|CB239990
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGC
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGC
EST: gi|211411458|gb|FL312810.1|FL312810
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTT
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTT
EST: gi|149074291|gb|EE162669.2|EE162669
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|33466593|gb|CF243642.1|CF243642
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|50333644|gb|CO528770.1|CO528770
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|60343169|gb|DN210142.1|DN210142
EST:     GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACA
EST: gi|26456321|gb|CA827904.1|CA827904
EST:     GAAGAAAACAAATGGATCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGC
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGC
EST: gi|20301313|gb|BQ164256.1|BQ164256
EST:     GAAGAAAACAAATGGATCAAACTGATCAAGCTATTGAGCGCTCAAAAATG                         GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTC
genomic: GAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTC

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), 49 (downstream exon)
Score: 456

AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 168

AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 313

AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgact ... tttcttgtagGTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATGgtgcgcgactaacatacacccttctcttttcttttttaaccatcaagtagaattacgctattgtttatagagcacaaattgattccacaaatccatatactcgggtagcctccattaaagagaaggaacaataagcttctccagctcttccataatggactttaaaggaaccattttcttgtag

- - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT