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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatcagtagcttttaatatttctaataaaatcctattggaacatcatacttataggatttaactttctcatcaatgtacctggatggttttacag

Basic information

species Zea mays
transcript GRMZM2G000718_T01
intron # 5
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 5
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 5'ss of exon 5
GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatcagtagcttttaatatttctaataaaatcctattggaacatcatacttataggatttaactttctcatcaatgtacctggatggttttacag
|||||| |||||||| |||||||||||||| |||||||| ||||| |||||||| |||||||| ||||  |   | |||||||||||||||||||||     |||| || | ||||   |  |||  | |   ||  |  | ||   |       |||   |||| | ||| | || | | |  || | |||
GTACCAAAGCAGCCTGGGTAATAAGAGGATTGAACTATTTGATACTGGTAATGATCAGGTGGCCGAGGACAACACTGTTCAAATGGCATCAGgtggtt----gtagtttcttatatcattgttaacctgcccctgagaggtaatgtgttc-----tta---ttctaaccaaagcactttggtaattcttcag
















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:     AACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: AACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|28361821|gb|CB240177.1|CB240177
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|6022470|gb|AW067503.1|AW067503
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCGCCGGAAGAAAACAAATGGATCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|149002889|gb|EE038886.2|EE038886
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|148941490|gb|EC886419.2|EC886419
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|21843414|gb|BQ703995.1|BQ703995
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCGCCGGAAGAAAACAAATGGATCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|37420501|gb|CF647941.1|CF647941
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|211541608|gb|FL367257.1|FL367257
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGGAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|60398834|gb|DN231650.1|DN231650
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|33466594|gb|CF243643.1|CF243643
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|71327359|gb|DR800293.1|DR800293
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|60349330|gb|DN216303.1|DN216303
EST:     TAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|148993116|gb|EE033716.2|EE033716
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|50333643|gb|CO528769.1|CO528769
EST:     TTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|149112851|gb|EE295664.2|EE295664
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|60352046|gb|DN219019.1|DN219019
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|149009782|gb|EE041679.2|EE041679
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|78117925|gb|DV536312.1|DV536312
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|149089650|gb|EE178904.2|EE178904
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|78083753|gb|DV512146.1|DV512146
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|211285641|gb|FL366666.1|FL366666
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAAATCA-GAACTCATTAGCAC
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAA-TCAAGAACTCATTAGCAC
EST: gi|91869534|gb|EB400432.1|EB400432
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|71327358|gb|DR800292.1|DR800292
EST:     TCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|30088413|gb|CB886618.1|CB886618
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|28361634|gb|CB239990.1|CB239990
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAA-GAACTCATTAGCACCGGAAGGAAACAAATGGACCAA
EST: gi|211411458|gb|FL312810.1|FL312810
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|149074291|gb|EE162669.2|EE162669
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|50333644|gb|CO528770.1|CO528770
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|60343169|gb|DN210142.1|DN210142
EST:     AATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
genomic: AATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|26456321|gb|CA827904.1|CA827904
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCGCCGGAAGAAAACAAATGGATCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA
EST: gi|20301313|gb|BQ164256.1|BQ164256
EST:     TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAG                         AAATGTCAAATCAAGAACTCATTAGCGCCGGAAGAAAACAAATGGATCAAA
genomic: TACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 405

GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 190

GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 236

GTACCAGAGCAGCCTTGGTAATAAGAGGATCGAACTATTCGATACGGGTAATGACCAGGTGGCTGAGGGAACTCCAGTTCAAATGGCATCAGgtggtcatca ... ggttttacagAAATGTCAAATCAAGAACTCATTAGCACCGGAAGGAAACAAATGGACCAAACTGATCAAGCTATTGAGCGCTCAAAAATG