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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactttgttactcataaagctagttcacattgatcgaagattcttgtagagataatatagttagtttgttttgatcttgcatggttcatggcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG

Basic information

species Zea mays
transcript GRMZM2G028730_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028730_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g20230.1 (Oryza sativa), 3'ss of exon 2
-tactttgttactcataaagctagttcacattgatcgaagattcttgtagagataatatagttagtttgttttgatc---ttgcatggttca-tggcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG
  |  |||| |  || |   ||     ||| |  | ||   ||| ||   | ||   ||  || |   |||| |||    |  |||| || | | | |  ||||| || |||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||| | |||||||||| || |||||| | ||| |||| |
tcatcttgtcatacacagctctg----acaatattagatctttcatggtaaaattgcatt-ttggggcgtttagattgcataacatgctttaattgaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGAAGTAGTCAGCTGACTTTAAAAGAACCATCAACCAATATGGTCTTAGCCG
















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|32922316|gb|CF027128.1|CF027128
EST:     CTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: CTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|211493208|gb|FL377894.1|FL377894
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGA
EST: gi|211366870|gb|FL423721.1|FL423721
EST:     GAAGCTTGAGGAAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAG
genomic: GAAGCTTGAGGA-GGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAG
EST: gi|91057201|gb|EB167619.1|EB167619
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAA
EST: gi|78109108|gb|DV527525.1|DV527525
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|78109107|gb|DV527524.1|DV527524
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTTTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|32913983|gb|CF018795.1|CF018795
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTGCACACCAGGGATTCATCAAAAAGTTGGCGTCA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCA
EST: gi|211420632|gb|FL480897.1|FL480897
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|28987245|gb|CB351535.1|CB351535
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|149085223|gb|EE174731.2|EE174731
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|19822283|gb|BQ048307.1|BQ048307
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGG
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGG
EST: gi|211443776|gb|FL403729.1|FL403729
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGGAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCANGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|211105668|gb|FL427080.1|FL427080
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTCTTCTGATGCGGTGATTCAG                         TTACACACCAGG-ATTCATCAAAAAGTTGGCGTCAGGCTGGATCAG
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAG
EST: gi|32849729|gb|CD989410.1|CD989410
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTGCACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|93280885|gb|EB673149.1|EB673149
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|37380718|gb|CF627188.1|CF627188
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
EST: gi|76917162|gb|DV166707.1|DV166707
EST:     AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAG                         TTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGA

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: 102

GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 224

GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

GTCGATAACAAGAAGCTTGAGGAGGCCGTCAAGGGGAAGTTTTCTGATGCGGTGATTCAGgtacgtgtct ... gcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagagataatatagttagtttgttttgatcttgcatggttcatggcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG
                       ttttgat  putative branch site (score: 145)
      ataatatagttagttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactttgttactcataaagctagttcacattgatcgaagattcttgtagagataatatagttagtttgttttgatcttgcatggttcatggcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - -tgttact
- - - - - - - - - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgg