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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacctgtctatcctgtccccccatcttctcacctcgtcaccttccatctactagtacagctgtacagggctagcttcgacagttgcctggctgg...

Basic information

species Zea mays
transcript GRMZM2G106928_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106928_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g44770.2 (Oryza sativa), 5'ss of exon 1
AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacctgtctatcctgtccccccatcttctcacctcgtcaccttccatctactagtac-agctgtacagggctagcttcgacagttg-cctggctgg--
||||||||||||||||| |||||||| ||||||||||| ||||| ||||||||| | ||  |||| ||||| || ||||| ||||| ||||| ||| | ||| |  ||||   ||   ||    |    |||| | |  |     || ||| ||||| | ||| | ||  ||  |   ||||||  |   |    |   |||  
AGGGCGCTCGTCGTCGCCGACGCCACCAAGAAGGCCGTCGCCGTGCTCAAGGGCACCTCCCAGGTTGAGGGAGTCGTCACCCTCACCCAGGATGACCAAGgt-cactacccacctgctctccttctttctcttgtaattttactgccctcc-tctacgactaccaactagactaga--agcttcatcgcctaatttaattggcc

upper sequence: GRMZM2G106928_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G19840.3 (Glycine max), 5'ss of exon 1
AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacctgtctatcctgtcccc--ccatcttctcacctcg-tcaccttccatctactagtacagctgtacagggctagcttcgacagttgcctggctgg
| | | |||  ||||   | |||||| ||||||||||| ||||||||||||||  | || |  ||||| ||||| | ||| ||||  || || ||||||||| ||   | | ||    |  |  |     ||  | | |  ||| | |   || |  |  |    ||  || |||    | |     ||   ||| |      
AAGCCCCTCACCGTCTTCGCCGCCACCAAGAAGGCCGTCGCCGTCCTCAAGGGGACCTCCGCCGTCGAAGGCGTCGCCACTCTCATCCAAGAAGACGATGgttcgccccttctcctctccttagcaaataattattttaattcgattaaaatcgaaatggtgc--caaatgcacaataatggaactaactaatgcatcttca-
















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|76909357|gb|DV163347.1|DV163347
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|32858163|gb|CD997844.1|CD997844
EST:     GCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|149048831|gb|EE048331.2|EE048331
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|211358170|gb|FL056486.1|FL056486
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|211360837|gb|FL056506.1|FL056506
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|211358174|gb|FL056490.1|FL056490
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|71430440|gb|DR811490.1|DR811490
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|14701400|gb|BI233818.1|BI233818
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|110505087|gb|EE017532.1|EE017532
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|149100116|gb|EE186171.2|EE186171
EST:     GGGCGCGTTTGAGGTTGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|149105223|gb|EE290711.2|EE290711
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|15208763|gb|BI430647.1|BI430647
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|211358167|gb|FL056483.1|FL056483
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|89247199|gb|DY618985.1|DY618985
EST:     GGGCGCGTCTGAGGTTGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|60355203|gb|DN222176.1|DN222176
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|15199132|gb|BI423675.1|BI423675
EST:     CACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: CACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|93014758|gb|EB640278.1|EB640278
EST:     GGGCGGGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGGCGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|71763838|gb|DR961775.1|DR961775
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|76016343|gb|DT943513.1|DT943513
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|60336753|gb|DN203726.1|DN203726
EST:     GGGGGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|78022822|gb|DV491209.1|DV491209
EST:     CGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: CGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|60352737|gb|DN219710.1|DN219710
EST:     CGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: CGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|211360826|gb|FL056495.1|FL056495
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATKTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|148944556|gb|EC889680.2|EC889680
EST:     GGGCGGGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGGCGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|76909356|gb|DV163346.1|DV163346
EST:     TGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: TGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|31355089|gb|CD439446.1|CD439446
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGTATTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|211363487|gb|FL056511.1|FL056511
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|31357015|gb|CD441372.1|CD441372
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|71763886|gb|DR961823.1|DR961823
EST:     GGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|71318465|gb|DR795998.1|DR795998
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
EST: gi|14701399|gb|BI233817.1|BI233817
EST:     GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATG                         GACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG
genomic: GGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATG

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: 232

AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATGGCTTCCACCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 460

AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATGGCTTCCACCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 171

AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATGGCTTCCACCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

AGGGCGCTCGTCGTCGCGGACGCCACTAAGAAGGCCGTAGCCGTCCTCAAGGGCGCGTCTGAGGTCGAGGGCGTGGTCACGCTCACGCAGGACGACGATGgtgcgttacc ... tgtataacagGACCTACAACTGTGAATGTCCGTATCACTGGACTTACCCCTGGACTTCATGGCTTCCACCTC