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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagatgtccatgtaccacaatgatcttgctgtgcatgcatagttttagagtaatttggtagaattgtaaggtatattatgtggtgaactttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 9
gtaagagatgtccatgtaccacaatgatcttgctgtgcatgcat--agttttagagtaatttggtagaattgtaaggtatattatgtggtgaactt--tattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT
||||| ||||   |  | | |   |  |     | || ||   |  | | ||   ||  | | | || | ||||   |  | ||  | || ||  |  |||| |||||||||||| |||||||||||||||||||| ||||||||||| || || || ||| ||||||||||||||||||||||| ||||||||||||| ||||||
gtaagggatggataaattcaaatgttttgccaatttgaattgttgaactattgtggtgctattgaagcaatgtagcatggaataatttgtaaatatgctatttcagGCAGGTTCTGCTAGAGATGGAGGAAGAATACATAAAGAACCTCTGTGCGCAGATTTTAAAATTCAAGCCTGATTTAGTTGTCACAGAGAAAGGTCTCAGT
















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|22715758|gb|BU197945.1|BU197945
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
EST: gi|31360791|gb|CD445148.1|CD445148
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
EST: gi|33093522|gb|CF053516.1|CF053516
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
EST: gi|32932045|gb|CF036857.1|CF036857
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
EST: gi|32930502|gb|CF035314.1|CF035314
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
EST: gi|24934892|gb|CA453110.1|CA453110
EST:     ACCAACGCTGAATTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: ACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
EST: gi|32934453|gb|CF039265.1|CF039265
EST:     AAGAAAGGAGAAAATCAGACCAACGCTGAGTTGATGAAGGAAGAAGATTG                         GCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA
genomic: AAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 349

GAAAGATAGTTAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GAAAGATAGTTAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 107

GAAAGATAGTTAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GAAAGATAGTTAACCCCCGTATCATCCTGTTGGACTGCCCTGTTGAGTATAAGAAAGGAGAAAATCAGACCAACGCTGAATTGATGAAGGAAGAAGATTGgtaagagatg ... tttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagagtaatttggtagaattgtaaggtatattatgtggtgaactttattgcagGCAGGTTCTCCTAGAGATGGAGGAAGAATATATAAAGAACCTTTGCGCTCAAATTCTAAAATTCAAGCCTGATTTAGTTATCACAGAGAAAGGGCTCAGT
                                            ctttatt  CT-rich tract
                            tatattatgt  TA-rich tract