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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctttctttacccactttttcgttctacgcatgtcattttgtggtatatcatatatgtattcttcttaggaaaaacattcagagcatatctttgttaagtctgaattttcattgccatttattttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA

Basic information

species Zea mays
transcript GRMZM2G051842_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051842_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 4
---gtgcctttct--ttac-ccactttttcgttctacgcatgtcattttgtggtat-atcatatatgtattcttcttaggaaaaacattcagagcatatctttgttaagtctgaattttcattgccatt-tattttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA
   || | ||||   |||| |||| || |      ||  ||  ||   | || ||  |||| | |   | ||||  || |  |   | | |     | | ||| || |    |||| ||  ||| |||  |  | | ||||||||| |  ||||  ||||||||  ||||||||||||||||||  ||||||||||||||||||||||||| ||||| || ||||||||||| |||||||| |
gtggtccttttcctcttacgccacattctgtgcacacaaattccagcatatgttaccatcacacaaaaaatcttactatgtca--taataaatatgtttattttttgacatggaatgttt-ttgtcatcatgatgtaatgcagTGGTTGGTTGTACGATATGCAAGACAGAACATGGAACAGATCCTTGAAGCTATTAGGATTGCTAAACAAGAAGGTCTCTCAGTATCATTGGATTTGGCTA
















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|71446345|gb|DR827395.1|DR827395
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|60338856|gb|DN205829.1|DN205829
EST:     ACAGGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: ACAGGCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|91057161|gb|EB167579.1|EB167579
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|76293563|gb|DV033131.1|DV033131
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|76286678|gb|DV026246.1|DV026246
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCCAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|71771409|gb|DR969346.1|DR969346
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|78105422|gb|DV523840.1|DV523840
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|148987163|gb|EE030992.2|EE030992
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|71447665|gb|DR828715.1|DR828715
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|78103938|gb|DV522356.1|DV522356
EST:     AAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: AAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|149088934|gb|EE178077.2|EE178077
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
EST: gi|148959742|gb|EC905640.2|EC905640
EST:     GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAG                         TGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT
genomic: GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCT

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), 39 (downstream exon)
Score: 277

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 65

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 99

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 130

GCCAATGAATTTAGAAAGGAGGATTTCAAAGGCTCCAAGgtgcctttct ... tttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagagcatatctttgttaagtctgaattttcattgccatttattttgatgcagTGGCTTATTGTGAGATATGCACAACAGAACATGGAACAGATTATTGAAGCTATTAGGATTGCTAAACAGGAAGGCCTTTCAGTATCATTAGATTTGGCCA
                                            ttttgat  putative branch site (score: 130)
                                        tttatttt  CT-rich tract
                                       atttattttgat  TA-rich tract