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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctgataaccttttcaacgatgacattgtgagctcatatggttgttactgaaactttggaagctgccgcag

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G329306_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g11320.1 (Oryza sativa), 5'ss of exon 7
CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctgataaccttttcaacgatgacattgtgagctcatatg-gttgttactgaaactttggaagctgccgcag
  ||||| ||| ||||||| |||||||||||||||||||||||||||  |  ||| | |||   || ||  |||    ||  | || |||||  |   | || ||       |||
GAGGAATTAAACGAGAGCTAGCTGCTGCAAAGAAGAAGgtcagtctgtaattcttgtgaacctaga-atcttga-taaatgcgcgtcgttaccaactatatgcaaatgattacag
















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|71329028|gb|DR801213.1|DR801213
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|211484888|gb|FL049377.1|FL049377
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|113703884|gb|EE681388.1|EE681388
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|211517927|gb|FL479799.1|FL479799
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|149051834|gb|EE155961.2|EE155961
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|78124365|gb|DV542749.1|DV542749
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|88756259|gb|DY540400.1|DY540400
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|76017867|gb|DT945037.1|DT945037
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|88756258|gb|DY540399.1|DY540399
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
EST: gi|211145441|gb|FL467393.1|FL467393
EST:     CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAG                         ATTGCTGACAGAAGAGAT-AGGAGCGGAAGGCATTTGCTAGGATTTTCCAA
genomic: CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAA

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), 49 (downstream exon)
Score: 126

CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 239

CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctga ... gctgccgcagATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGAATCAAAAGAGAGCTGGCTGCTGCAAAGAAGAAGgtcagtctgataaccttttcaacgatgacattgtgagctcatatggttgttactgaaactttggaagctgccgcag

- - - - - AAGAGA
- - - - - -  AGAGCT
- - - - - - - - - - GCTGCT
- - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - AAGAAG