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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCTCCTCGCCTTCGCCTGCAGCTCCAGCTCCGGACGGGTGGTGGTCACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgcccgcgtggcgtgtctactagtagtatcctccttcttcttcttcattcattcatcctggtggtgtactactagactactactagtagctcacgcgcgcggcacatgtagatgtagcctctaaccaccgttgctgccctgaaactcaaaacgaag

Basic information

species Zea mays
transcript GRMZM2G471269_T04
intron # 1
splice site 5'
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|211339195|gb|FL410612.1|FL410612
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211317844|gb|FL424598.1|FL424598
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTAC
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTAC
EST: gi|211361158|gb|FL409334.1|FL409334
EST:     ACTAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211319633|gb|FL415404.1|FL415404
EST:     ACCAGCTTGCCTG-CTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211219464|gb|FL394121.1|FL394121
EST:     ACCAGCTTGCCTG-CTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211284434|gb|FL407065.1|FL407065
EST:     ACTAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|71437541|gb|DR818591.1|DR818591
EST:     ACCTGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCTAAACAGG                         GTAAGTGAAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTAC
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTAC
EST: gi|211458639|gb|FL385383.1|FL385383
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211348131|gb|FL378229.1|FL378229
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211073389|gb|FL369067.1|FL369067
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211343693|gb|FL394263.1|FL394263
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211214594|gb|FL385235.1|FL385235
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211357904|gb|FL385739.1|FL385739
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
EST: gi|211425791|gb|FL370217.1|FL370217
EST:     ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGG                         GTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT
genomic: ACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGT

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: 43 (upstream exon), 46 (downstream exon)
Score: 17

TGCTGCTCCTCGCCTTCGCCTGCAGCTCCAGCTCCGGACGGGTGGTGGTCACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGTCCAGGCCGAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

TGCTGCTCCTCGCCTTCGCCTGCAGCTCCAGCTCCGGACGGGTGGTGGTCACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGTCCAGGCCGAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 131

TGCTGCTCCTCGCCTTCGCCTGCAGCTCCAGCTCCGGACGGGTGGTGGTCACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGTCCAGGCCGAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 78

TGCTGCTCCTCGCCTTCGCCTGCAGCTCCAGCTCCGGACGGGTGGTGGTCACCAGCTTGCCTGGCTTCGACGGCGACCTCCCCTTCCACCTCGAAACAGGgtgcgcgtgc ... caaaacgaagGTACGTGGAGGTGGAGGAGGACGCCGGCGTGGAGCTCTTCTACTACTTCGTCCAGGCCGAGTCCGGCGCCGCCGCCGCCGCCGATGACACCCCTTTCCTC