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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatctagtatcctctaggactgaacaatttcaattgttcatgaaccacttatctatgtattgctaattctggtgtttggtgtgtttcag

Basic information

species Zea mays
transcript GRMZM2G047564_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 5'ss of exon 8
AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatctagtatcctctaggactgaacaatttcaattg---------------ttcatgaaccacttatctatgt--------attgctaattctggtgtttggtgtgtttcag
|||| |  | ||||| |||||||||||||| |||||||| || || ||||| ||||||||||||||||||||| ||| || |||||||||| |||| ||||| |||  ||  |||||| ||  | |||| | ||| | |||               |||| |   | ||| |   | |        |||||||||||||   |||||| |||| |||
AGGACTCAAAAAAGGGGCTCCATTTTCTCTATGTTTAACTCAAAAACATTTTTCTCAAGTTGCATCAGCATATAGGAATAATGAACACTATCTATCGAAGgtatga--ctgctatcctgtacaattgaatacttttatttggttaactattttattttcaggcttctctttttcttttgcaaggacattgctaattctgacatttggtttgtt-cag

upper sequence: GRMZM2G047564_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv11s0016g04290.t01 (Vitis vinifera), 5'ss of exon 10
AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaa------tctagtatcctctaggactgaacaatttcaattgttcatgaaccacttatctatgtattgctaattctg----gtgtttggtgtgtttcag-----------------
|||  |||  || || ||||| |||||||||||||||||||| |||||||||||   |||||| |  |||  ||| |  | |||     |||| |  |  ||| |        ||  |  |  | |       ||  |    ||   ||  |   | | ||  | |       | |||| |     ||    ||| | || | |                 
AGGTCTTGGAAAGGGGGCTCCTTTTTCTCTTTGTTTAACACAAAAGCATTTCTCCAGAGTTGCTTTGGCACGTGGAAAAAATGACAGTGATTTGTGCAGTgtgagttgctttttcctgcttttttttttttataaagaaaagaaaacttattttgctaattcccaaaaggccacaaattttaagaagtaacgggtattttcctgcaattggctgtatccag
















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|76012489|gb|DT939659.1|DT939659
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|71312657|gb|DR792849.1|DR792849
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|60398946|gb|DN231762.1|DN231762
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|18166670|gb|BM336509.1|BM336509
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|78083152|gb|DV511545.1|DV511545
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|78078184|gb|DV506599.1|DV506599
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|88750160|gb|DY534301.1|DY534301
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|60346890|gb|DN213863.1|DN213863
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|60345004|gb|DN211977.1|DN211977
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|76280673|gb|DV020241.1|DV020241
EST:     TCTTTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|37379970|gb|CF626760.1|CF626760
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|149097994|gb|EE183939.2|EE183939
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211171388|gb|FL176740.1|FL176740
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|76012490|gb|DT939660.1|DT939660
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|18165516|gb|BM335355.1|BM335355
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|60399515|gb|DN232327.1|DN232327
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|91873503|gb|EB403460.1|EB403460
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTGGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211528664|gb|FL445658.1|FL445658
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211171385|gb|FL176737.1|FL176737
EST:     TATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|211171387|gb|FL176739.1|FL176739
EST:     ATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: ATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|71331740|gb|DR802726.1|DR802726
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
EST: gi|88749306|gb|DY533447.1|DY533447
EST:     TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATTTAAG                         CTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT
genomic: TCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 73

AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC


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

AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

AGGAATTGAGAAAGGCGCTCCATTTTCTCTTTGTTTAACACAGAAGCATTTCTCTCAAGTTGCATCAGCATATGGGACTAGTGAACACTATTTATCTAAGgtgtgaatct ... tgtgtttcagCTGGCTGGTGTTATGAAATTGGAATATCGCATTGCCTTGAGGTCGTCGATTAGAAACGATTTTGTTGAAGGTGTGCGTGCTGTTTTAGTTGACAAGGACC