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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTGCGGGTGCGGCTCCTCCTCGCCGACGGCGCCAGCGCCGCCTCCCTCGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgacttctcactcggcagcccccctccccgctcctcttcctcgcacgtcttcgcgttccaacggatgtgacatttcctcgcgaatccacggctcct...

Basic information

species Zea mays
transcript GRMZM2G044569_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|78085525|gb|DV513918.1|DV513918
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAG                         TGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|71766873|gb|DR964810.1|DR964810
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|71764260|gb|DR962197.1|DR962197
EST:     CGCCCTCTCGACATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|89253176|gb|DY624962.1|DY624962
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAG                         TGGTTGCAGTGAAAACTATAAGGAAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|71449470|gb|DR830520.1|DR830520
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAG                         TGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|78075719|gb|DV504153.1|DV504153
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAG                         TGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|78085425|gb|DV513818.1|DV513818
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|74242907|gb|DT650821.1|DT650821
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAG                         TGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|91875640|gb|EB405597.1|EB405597
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|149051784|gb|EE155909.2|EE155909
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|76287272|gb|DV026840.1|DV026840
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|91877670|gb|EB407627.1|EB407627
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAG                         TGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
EST: gi|26457371|gb|CA828954.1|CA828954
EST:     CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGT-C-C--                         -----GCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC
genomic: CGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAAC

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: 49 (upstream exon), 48 (downstream exon)
Score: 33

GACGTGCGGGTGCGGCTCCTCCTCGCCGACGGCGCCAGCGCCGCCTCCCTCGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAACAACGAACTGGAAGAGGTGGTCCCAAATGACTCGGACCCTCTTATTGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24

GACGTGCGGGTGCGGCTCCTCCTCGCCGACGGCGCCAGCGCCGCCTCCCTCGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAACAACGAACTGGAAGAGGTGGTCCCAAATGACTCGGACCCTCTTATTGGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 8

GACGTGCGGGTGCGGCTCCTCCTCGCCGACGGCGCCAGCGCCGCCTCCCTCGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAACAACGAACTGGAAGAGGTGGTCCCAAATGACTCGGACCCTCTTATTGGGA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 36

GACGTGCGGGTGCGGCTCCTCCTCGCCGACGGCGCCAGCGCCGCCTCCCTCGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgactt ... gtgattgaagTGGTTGCAGTGAAAACTAGAAGGGAAGAACAGCCTCCTAATGGATAGGAACAACGAACTGGAAGAGGTGGTCCCAAATGACTCGGACCCTCTTATTGGGA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTGCGGGTGCGGCTCCTCCTCGCCGACGGCGCCAGCGCCGCCTCCCTCGCCCTCTCGGCATAGACCGGCGACGGTAGCTGCATCTTCGAGTCCGCAGgtgctgacttctcactcggcagcccccctccccgctcctcttcctcgcacgtcttcgcgttccaacggatgtgacatttcctcgcgaatccacggctcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC