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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcatgagctcttaccatctggcagtttattttcccacatcgatcgtacataacagtagaacgtgacgtgctcaggctggcttaccttcttgacacttcagtacttcactttgccaaaacgttcacggcggttgcttgtttgcctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAGAAGGCTGAATTGCGTGTTTGTGGTTGAACATTTGTGCATATGTGCTTGT

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 9
splice site 3'
intron type U2

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|453304|gb|T15278.1|T15278
EST:     CAATGGACGACGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|86470328|gb|DY236698.1|DY236698
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|18179571|gb|BM380781.1|BM380781
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|211295447|gb|FL439736.1|FL439736
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|78113030|gb|DV531424.1|DV531424
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|148971663|gb|EE022386.2|EE022386
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTCCCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|50331764|gb|CO526890.1|CO526890
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTTTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|5871660|gb|AW018131.1|AW018131
EST:     CAATGGACGTCGACCTTGGCAGTCCAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCCCCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|76013820|gb|DT940990.1|DT940990
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|4573046|gb|AI586695.1|AI586695
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCCCCCTACCAGAAGGCGCAGGAAA
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|60341702|gb|DN208675.1|DN208675
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         TTCTGTCACTTGGCTCGGGAAAAGGAAGCACCCTACCCTACCAGAAGGCGC
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCT-TGTCACTTGTCTCGGGAAAAGGAAGCACCCTACC--A---GAAGGCGC
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|211502356|gb|FL413772.1|FL413772
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|78022213|gb|DV490600.1|DV490600
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|110482572|gb|EE011367.1|EE011367
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTTTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|60393918|gb|DN226788.1|DN226788
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|37374451|gb|CF623583.1|CF623583
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|4572984|gb|AI586633.1|AI586633
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|6056893|gb|AW091298.1|AW091298
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|101388963|gb|EB816463.1|EB816463
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|78077260|gb|DV505694.1|DV505694
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
EST: gi|15100603|gb|BI396394.1|BI396394
EST:     CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTTAAG                         CTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG
genomic: CAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAG

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), 45 (downstream exon)
Score: 49

ATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAGAAGGCTGAATTGCGTGTTTGTGGTTGAACATTTGTGCATATGTGCTTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

ATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAGAAGGCTGAATTGCGTGTTTGTGGTTGAACATTTGTGCATATGTGCTTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

ATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAGAAGGCTGAATTGCGTGTTTGTGGTTGAACATTTGTGCATATGTGCTTGT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 92

ATTTTTGAAATTCATAGCGACAGTCATACCGACTATTGAGTACGATTATACAATGGACGTCGACCTTGGCAGTACAAGCTGATTATTGGTTGGCTTGAAGgtaaagcatg ... ctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAGAAGGCTGAATTGCGTGTTTGTGGTTGAACATTTGTGCATATGTGCTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtacttcactttgccaaaacgttcacggcggttgcttgtttgcctgttgtcagCTTGTCACTTGTCTCGGGAAAAGGAAGCACCCTACCAGAAGGCGCAGGAAGAAGGCTGAATTGCGTGTTTGTGGTTGAACATTTGTGCATATGTGCTTGT
                                        tttgcct  CT-rich tract