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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgcttgcctagtctaattgccccttacctgggtgaatatctggcattcttagattagatttaagaaaatgtggtgttagtagtagtagtagta...

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 4
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 4
lower sequence: LOC_Os06g11320.1 (Oryza sativa), 5'ss of exon 4
ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgcttgcctagtctaattgccccttacctgggtgaatatctggcattcttagattagatt--taagaaaatgtggtgttagtagtagtagtagta--
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AGAAGAGCTCAGCACTGCGGAAGACCAAATCGATTATACTCACAAATAGCTCTgtaagttgcattatctattccagtaacttatt-tgtggatgaacgttttg---tcttaaaggaaactgttattgtcattttatattatcatgagttacctctgc
















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:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     AGAGCGCAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|113703884|gb|EE681388.1|EE681388
EST:     GGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: GGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|78124365|gb|DV542749.1|DV542749
EST:     CAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: CAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|32794497|gb|CD946733.1|CD946733
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTA
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTA
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     AGAGCTCAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|88756259|gb|DY540400.1|DY540400
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|32865832|gb|CF005514.1|CF005514
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGGCAA-TTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGA
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATG-CAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGA
EST: gi|76017867|gb|DT945037.1|DT945037
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     AGAGCNCAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCC                         GCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT
genomic: AGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGAT

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: 38 (upstream exon), 46 (downstream exon)
Score: 163

ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 154

ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 218

ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 358

ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgc ... actttttcagGCATGCAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAGAGCACAGCACTGCGGAAGACCAAGTCAATAATACTCACTAATAGCTCCgtatgttcgcttgcctagtctaattgccccttacctgggtgaatatctggcattcttagattagatttaagaaaatgtggtgttagtagtagtagtagta

-  AGAGCA
- - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaat