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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgacattttggaagtgataatttagctttctgtctttcttttactgttctaatcattgctacctagtgattttgtattccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA

Basic information

species Zea mays
transcript GRMZM2G096343_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 2
gttgacattttggaagtgataatttagctttctgtctttcttttactgttctaatcattgctacctagtgattttgtattccttcgt-tagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA
|||  | |  ||||| ||| || |||    | |||  ||  |  |  ||      |||| ||||| ||||| |   ||||||||  | ||||||||||||||| ||||||||||| | |||||||||||||||||||||| ||||||||||   |||||| ||||||| |||||||| |||||||| ||||
gttagcttactggaaatgacaaattaatagtttgtgatttctcgatggtgtcctacattcctacccagtgactgattattcctttatctagGTTGCTGGAGATGTTTTGTTAGTGCAAAGGGGAAACTGTAAGTTCACTAAAAAAGCTAAGAATGCTGAAGCTGCTGGGGCTTCTGCTATTATAATCATCA
















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|149049844|gb|EE048531.2|EE048531
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|89758526|gb|DY687677.1|DY687677
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|76282122|gb|DV021690.1|DV021690
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|211324017|gb|FL189571.1|FL189571
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|211297692|gb|FL447045.1|FL447045
EST:     ACTTGCTGTTAGCAGACCTTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|211324014|gb|FL189568.1|FL189568
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTA
EST: gi|148956514|gb|EC902353.2|EC902353
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|149081128|gb|EE170234.2|EE170234
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
EST: gi|71422117|gb|DR805619.1|DR805619
EST:     ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAG                         GTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA
genomic: ACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACA

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: 47 (upstream exon), 49 (downstream exon)
Score: 88

TCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCAACTGGACAAACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

TCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCAACTGGACAAACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

TCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCAACTGGACAAACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 127

TCGATTTGGCCCCAAGATAGAGTCAAAGGAAAAGCATGCCAACTGGACAAACTTGCTGTTAGCAGACCCTTCTGATTGCTGCACCCCTCCAAGAGAGAAGgttgacattt ... ccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcttttactgttctaatcattgctacctagtgattttgtattccttcgttagGTTGCTGGAGATATTTTGTTAGTGGAGAGGGGAAACTGTAAGTTCACTACAAAAGCTAAGGTGGCTGAATCTGCTGGTGCTTCTGCGATTATAATTATCA
             ttctaat  putative branch site (score: 127)
                                    ttttgtattccttc  putative PPT
                                   attttgtatt  TA-rich tract