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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggttgtcctgtttcatagcatgtttttctcagttctcagtcatattgcagaagtcagctgtgacatttctatctatcaaataaaaaaaatatttgcatgtcgggttcatgatctgctattgtttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA

Basic information

species Zea mays
transcript GRMZM2G006277_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006277_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g67730.1 (Oryza sativa), 3'ss of exon 3
----------------gtgagggttgtcc-tgtttcatagcatgtttttctcagttctcagtca---tattgcagaagtcagctgtgacattt--ctatctatcaa------------------ataaaaa---aaatatttgca------tgtcgggttcatgatctg--ctattgtttgcgt-gtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA
                | ||   | ||     |   | |  |    |  | || || ||| | |   || |   ||| |  | |||| ||| |       ||| ||                  |||||||   | || ||||        | |      | |||| ||  |  || |||| |    |||||||| |||||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||| || || |||||||||| | ||||||| ||||||
gtaagggtcttatgatgggaatatcgtttgcatgctaaaaaaatcatggcacatttttcacttacaataataaggaaattggttgtggcatctagtcgcttataaacaattggacttttcttctataaaaagagagatttttgttcttttctcttcaacgcctgatatgaccagttatttgtgccacagGATACTATTTGATGATTTGCACAAGACGGGGATCTTCACATGGGATTACTTGCATCATCTGGGTTCTAAAAAGTTCAGTCTGACGCGAAATTATATCAGA

upper sequence: GRMZM2G006277_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10430.2 (Oryza sativa), 3'ss of exon 3
gtgagggttgtcctgtttcatagcatgtttttctcagttctcagtcatattgcagaagtcagctgtgacatttctatctatcaaataaaaaaaatatttgcatgtcgggttcatgatctgctattgtttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA
                                    ||   || |  | |||  |   |    | ||   ||  | | |          || ||||   | |||||      |||| ||  |||| | |   || |||||| | ||||||||  ||||||||||||||||||| |||||||||||||||||||| || ||||| ||||| ||  |||||||| |||  || |||| |
------------------------------------gtaagcaattct-ttgtggcttttta-tatgcacttcttgtttgattttccgcaagaataca-gtatgtctataatatgacctagtatt-tgtat-tgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTTGCACCACCTAGGTTCTAACAAGTTTGGTCTGATGCGAAGCTATATCACA

upper sequence: GRMZM2G006277_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10430.1 (Oryza sativa), 3'ss of exon 3
--------------------------------gtgagggttgtcctgtttcatagcat--gtttttctcagttctcagtcata--ttgcaga-agtcagctgtgacatttctatctat-caaataaaaaaaatatttgcatgt------cgggttcatgatctg--ctattgtttgcgt-gtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA
                                |||  |||| |||     ||||   |   ||  ||    |||  |   | |  | | |   | |    |||| | ||| ||| |   |   |      | | |  ||| |          ||  || || ||  ||| | ||||  | | |||||| | ||||||||  ||||||||||||||||||| |||||||||||||||||||| || ||||| ||||| ||  |||||||| |||  || |||| |
gtgagggtcatgtttcttgcattatcaaattcgtggaggttttccc-ccacataatgtcaattgatcctgtttcgtaaaaaaaaatagtaagcaattctttgtggc-tttttatatgcacttcttgtttgattttccgcaagaatacagtatgtctataatatgacctagtatttgtattgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTTGCACCACCTAGGTTCTAACAAGTTTGGTCTGATGCGAAGCTATATCACA

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|211392362|gb|FL377415.1|FL377415
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|18172861|gb|BM348249.1|BM348249
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|211443955|gb|FL410275.1|FL410275
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|211108340|gb|FL388580.1|FL388580
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTCTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|18167915|gb|BM337755.1|BM337755
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|211301554|gb|FL430309.1|FL430309
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|211321452|gb|FL399586.1|FL399586
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|18176507|gb|BM351440.1|BM351440
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|67021891|gb|CO450640.1|CO450640
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|211057895|gb|FL423513.1|FL423513
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
EST: gi|211220783|gb|FL456545.1|FL456545
EST:     CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCG                         GATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT
genomic: CGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTT

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: 46 (upstream exon), 49 (downstream exon)
Score: 6

GTTATATTTGGACGACGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 13

GTTATATTTGGACGACGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 2

GTTATATTTGGACGACGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 4

GTTATATTTGGACGACGACATGTTGGGATAATGTCAGCTGAATCAGTAGGAAACTACGGAGTCCGgtgagggttg ... ttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataaaaaaaatatttgcatgtcgggttcatgatctgctattgtttgcgtgtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA
     aaaaaaatatttgcat  TA-rich tract