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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatgaactgcatttgtagttgcaactcagtacgcatgctcctgttcaatttcctgataatccttgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT

Basic information

species Zea mays
transcript GRMZM2G051288_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g53710.1 (Oryza sativa), 3'ss of exon 4
gtaggatgaactgcatttgtagttgcaactcagtacgcatgctcctgttcaatttcctgataa-----tccttgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT
||||||| |||   | ||  ||   |     | |    ||  | |  | || ||| ||||| |     | ||||| ||||||||||||||  ||| |||||  || |||||||| || |||||||| ||||||||||||||| |||| ||||||||||| ||||||||||| 
gtaggataaacaataattaaagcaactcaatattgtatatctttcgctccattttgctgatgacagattacttgtcttgcagATTAAATATCGGAGCATGAGTCCAGAAGCAGCATTAGATCATGTCCGATCCATTAGGCCTAGAGTACTTTTGGCACCATCGCAGTGGCAG
















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|50332926|gb|CO528052.1|CO528052
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|149104022|gb|EE289453.2|EE289453
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCA
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCA
EST: gi|93014040|gb|EB639560.1|EB639560
EST:     TTGTAAAGCTGGAAGAGGACGAAGCCCCACTATTGTATTGTGCTACCTTG                         ATTAAATACAGGAACCTGACCCCCTGAC-CACCTTTGGATCATGTACGAT
genomic: TTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTAC-TTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCC-TGAAGCAGCTTTGGATCATGTACGAT
EST: gi|67018199|gb|CO446948.1|CO446948
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|71444037|gb|DR825087.1|DR825087
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|148985353|gb|EE029663.2|EE029663
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGAT
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGAT
EST: gi|101385912|gb|EB815004.1|EB815004
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|71766290|gb|DR964227.1|DR964227
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|211298370|gb|FL254614.1|FL254614
EST:     TGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: TGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|91055876|gb|EB166294.1|EB166294
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|78119952|gb|DV538336.1|DV538336
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|148952076|gb|EC897867.2|EC897867
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTA
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTA
EST: gi|67020173|gb|CO448922.1|CO448922
EST:     ATTGTAAAGCTGGAAGAGGACGAAACACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
EST: gi|71331076|gb|DR802368.1|DR802368
EST:     ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG                         ATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC
genomic: ATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCC

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), 49 (downstream exon)
Score: 92

GGAATGCATCACAAGGCGGTACTACATATGTTCATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

GGAATGCATCACAAGGCGGTACTACATATGTTCATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 110

GGAATGCATCACAAGGCGGTACTACATATGTTCATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GGAATGCATCACAAGGCGGTACTACATATGTTCATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTGgtaggatgaa ... tgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaactcagtacgcatgctcctgttcaatttcctgataatccttgtgttgcagATTAAATACAGGAACATGACCCCTGAAGCAGCTTTGGATCATGTACGATCCATTAGGCCTCGAGTGCTTTTGGCACCCTCGCAGTGGCAT
                                tcctgat  putative branch site (score: 95)
                                         tccttgt  putative PPT
                         ttcaattt  TA-rich tract