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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcatgcggaatcttggcctgtattattgtatggcaacatatgaacttaactaactgaaactttgtatcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG

Basic information

species Zea mays
transcript GRMZM5G816356_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816356_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g47690.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------gca-agcatgcggaatcttggcctgtattattgtatggcaacatatgaact-taactaactgaaactttgtatcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG
                                                                                 || |  ||   ||| || |||    || ||  |    ||  |||||||   ||  || ||||   ||| |||| | |||||||||||||||||||||||||||| || ||||||||||  |||||||| ||||||||||| 
gcaagtatgcattatcctttttttaagactaaatacacatcagcttatagaatagcataccactttttttaggcaatcatacataatattttgaaactaggcacacatcatcttcatacataatatgaagggtaggtagctgacttttt-tatccttatcagATTTTCACATTGCCAAAGGATACCCTGCTTTATCCTGGCCATGACTACAAAGGTTTCACA

upper sequence: GRMZM5G816356_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv19s0135g00060.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------------------gcaagcatgcggaatcttggcctgtattattgtatggcaacatatgaacttaactaactgaaactttgtatcgtgatc-agATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG
                                                           |  | ||     ||         | ||  || |||   ||  | |       | | | | ||  |||  |   ||||| |||| |||||||| ||||||||| || |  | ||||||||||||||||| | ||||||||| 
gcaaggatacatcatgctcggtcatttgttcatgttgtaaataagtgagaaacagaaaagagaacacaaaaaaaaaaaaaaagaatctttttatcttaat-tctacctgccattgatttaatattttaaaattgatccagATATTCACATTACCAAAGGATGCATTGATATATCCTGCTCATGACTACAGAGGTTTCACT
















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|111990479|gb|EE331905.1|EE331905
EST:     GGCAGGAAGTTCTGAACAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GG-AGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|148944080|gb|EC889165.2|EC889165
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|108953804|gb|EC364896.1|EC364896
EST:     GGAGGAAGTTCTGAACAGTTGTATCAGTCAGTGCATTCACAG                         T
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcag-
EST: gi|108953804|gb|EC364896.1|EC364896
EST:     GGAGGAAGTTCTGAACAGTTGTATCAGTCAGTGCATTCACAG                         T
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcag-
EST: gi|149098018|gb|EE183965.2|EE183965
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|78180745|gb|DV551118.1|DV551118
EST:     GTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|78077487|gb|DV505921.1|DV505921
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|78077488|gb|DV505922.1|DV505922
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|93283010|gb|EB675274.1|EB675274
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|9953495|gb|BE640078.1|BE640078
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|60339336|gb|DN206309.1|DN206309
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|148930115|gb|EC872441.2|EC872441
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|78106798|gb|DV525216.1|DV525216
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATG
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATG
EST: gi|16917690|gb|BM073404.1|BM073404
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|32867553|gb|CF007235.1|CF007235
EST:     TGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: TGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|76911210|gb|DV164200.1|DV164200
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|71446301|gb|DR827351.1|DR827351
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|50331454|gb|CO526580.1|CO526580
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|71446302|gb|DR827352.1|DR827352
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTTATAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACT-ATAA
EST: gi|78106797|gb|DV525215.1|DV525215
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
EST: gi|211380540|gb|FL436905.1|FL436905
EST:     GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAG                         ATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA
genomic: GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAA

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: 42 (upstream exon), 47 (downstream exon)
Score: 78

GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 200

GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 265

GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 86

GGAGGAAGTTCTGAGCAGTTGTATCAGTCAGTGCATTCACAGgcaagcatgc ... tcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattgtatggcaacatatgaacttaactaactgaaactttgtatcgtgatcagATTTTCACATTGCCAAAGGATACACTACTTTATCCTGCTCATGACTATAAAGGTTTCACG
                          aactaac  putative branch site (score: 86)
                        ttaactaa  TA-rich tract