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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttcattgattcctcagttgtttcaggttgtaattgatcaactaaattaaggcaagttcagctgatcttctgtgcatgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g44070.2 (Oryza sativa), 3'ss of exon 7
gtgtttcattgattcctcagttgtttcaggttgtaattgatcaactaaattaaggcaagttcagctgatcttctgtgcatg----atg-cagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG
||  |    || |  | ||| |   | |  || |||    |||| |     ||| | || |  ||||| |  ||||| |||    ||| |||| |||||||| || ||||| ||||| |||||||||||||| |   ||||||| || ||||| || |||||||| ||||| || |||||||| || |||||
gtactgggctgttctcccagatccgtgaa-ttataaactgtcaatt----caagtctagattggctgaccccctgtgtatgtatgatggcagGTTTCAGGAATCAAATGCTCGATGCGGTGAGGGGTTTCTCCGGCGCAAGGCAGAACGGTCTTTTTATCAACTCCTGTTTCGCACATTGCCAAAGTGAGAG

upper sequence: GRMZM2G160569_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g01110.t01 (Vitis vinifera), 3'ss of exon 10
---------gtgtttcattgattcctcagttgtttcaggttgtaat--tga--tcaact---aaattaaggcaagttcagctgatcttctgtgcatgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG
          |   |  || | | |    | | || | | |  |||  ||   |||| |   |  || |      |     | ||  | |       |  |||  ||||| || || |||||  |||| || || || ||||| |  || |    |||||| || ||||| |||||||||||||||||||| ||||  |||||
gtggtttgcttagcttgtttacttcctcctggctttatgcttcaatcctggcttcaattttgatcttgatatttatgagtttcattcttttcatgcaaaacagATTTCAGAAAACAAATGCTAAATGCTGTAAGTGGCTTCTCAGGGTCCAAAAGAAATGGGCTATTCATAAACTCATGTTTTGCTCATTGTCAGACAGAGAG
















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|31998134|gb|CD661943.1|CD661943
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|148953387|gb|EE152881.2|EE152881
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTTTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|91056470|gb|EB166888.1|EB166888
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|60400656|gb|DN233463.1|DN233463
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|4887514|gb|AI677613.1|AI677613
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|5058593|gb|AI737069.1|AI737069
EST:     CAGCTCCAGTTTTTGCAAG                         GGTTCAGGANCCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: CAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|211266712|gb|FL294975.1|FL294975
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|101383816|gb|EB813963.1|EB813963
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTTTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|67018103|gb|CO446852.1|CO446852
EST:     TAGGACGAACCATGCCTTATGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTTANGAACCANATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|91051274|gb|EB161692.1|EB161692
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|31356908|gb|CD441265.1|CD441265
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|86471748|gb|DY238118.1|DY238118
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|93016716|gb|EB642236.1|EB642236
EST:     TAGGGCGAAGCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|149028341|gb|EE154630.2|EE154630
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|78025651|gb|DV494038.1|DV494038
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|149009226|gb|EE153857.2|EE153857
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGNNNNNNNGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|149101141|gb|EE187249.2|EE187249
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|76932739|gb|DV173141.1|DV173141
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
EST: gi|60401537|gb|DN234344.1|DN234344
EST:     TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAG                         GGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC
genomic: TAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGC

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), 47 (downstream exon)
Score: 150

CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG


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

CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

CAAAGTGTGGCCCCTAGAACAGCTGATCCCCAAGGTCTTTGGTCAAAGTGTAGGACGAACCATGCCTTCTGTAATAGCAACCAGCTCCAGTTTTTGCAAGgtgtttcatt ... catgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaattgatcaactaaattaaggcaagttcagctgatcttctgtgcatgatgcagGGTTCAGGAACCAGATGCTTGATGCCGTGAGGGGTTTCTCTGCATCAAGGCAAAATGGTCTGTTCATCAACTCATGTTTTGCTCATTGCCAGAGCGAGAG
       atcaactaaattaa  TA-rich tract