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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGCTCTACGACGACTAGTGGGCCGCCGGCGCTGGCGCCGCCTTACGCCAGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcatcccttttcttcacttcctgccgtgcgaagccgagcacccaaaccctaatctaaagctatttggctatttgttggttcctaacctggaacc...

Basic information

species Zea mays
transcript GRMZM2G102858_T01
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|87152292|gb|DY397081.1|DY397081
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
EST: gi|211525601|gb|FL330624.1|FL330624
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|211462421|gb|FL327914.1|FL327914
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|211520176|gb|FL353412.1|FL353412
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAAC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG--GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAAC
EST: gi|60340984|gb|DN207957.1|DN207957
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
EST: gi|211486952|gb|FL359770.1|FL359770
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|211049593|gb|FL335089.1|FL335089
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|33095169|gb|CF055163.1|CF055163
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|211512784|gb|FL351601.1|FL351601
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|113682230|gb|DW841315.1|DW841315
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAG
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAG
EST: gi|211350003|gb|FL351953.1|FL351953
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAAC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG--GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAAC
EST: gi|149079805|gb|EE168802.2|EE168802
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
EST: gi|18964868|gb|BM661256.1|BM661256
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
EST: gi|211385731|gb|FL321718.1|FL321718
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|148969766|gb|EE020648.2|EE020648
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
EST: gi|211541155|gb|FL350247.1|FL350247
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
EST: gi|22490262|gb|BU050185.1|BU050185
EST:     TCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
genomic: TCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCT
EST: gi|211228983|gb|FL343800.1|FL343800
EST:     AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAG                         CTGGNNNNNNNNTCTATAGCCAAACATAATAATGGCTATGATTGATGAACC
genomic: AGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGG-GAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACC

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), 46 (downstream exon)
Score: 81

CTCGCTCTACGACGACTAGTGGGCCGCCGGCGCTGGCGCCGCCTTACGCCAGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCTCTCTACCCGATTGCTGTACTGATTGATGAACTGAAAAATGAAGATATTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 53

CTCGCTCTACGACGACTAGTGGGCCGCCGGCGCTGGCGCCGCCTTACGCCAGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCTCTCTACCCGATTGCTGTACTGATTGATGAACTGAAAAATGAAGATATTC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 27

CTCGCTCTACGACGACTAGTGGGCCGCCGGCGCTGGCGCCGCCTTACGCCAGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCTCTCTACCCGATTGCTGTACTGATTGATGAACTGAAAAATGAAGATATTC


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 58

CTCGCTCTACGACGACTAGTGGGCCGCCGGCGCTGGCGCCGCCTTACGCCAGGTGCCGAGGTCTTCGTTGATCTCTTCGCCGGCGACGAGCACCCACCAGgtattctcat ... tattttacagCTGGGAAAAAATCTATAGCCAAACATAATAATGGCTATGATTGATGAACCTCTCTACCCGATTGCTGTACTGATTGATGAACTGAAAAATGAAGATATTC