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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctggatattttgacacaactagccggttttaagattcgttaaatgtgtttttagcttaaaatctgttgcgcag

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 5'ss of exon 15
GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctggatattttg-acacaa-ctagccggttttaagattcgttaaatgtgtttttagcttaaaatctgttgcgcag
|||||||||||| ||||| |  || || |||||||| || |||||||| ||||| |||||||| |||||||||||| | ||||||||||||| |   |||  | |||||  ||  |  ||| | | | |||||| | |||  |  | ||| |   ||        ||| ||||
GTACATTGAGTATTGCCGTGTTACTTGTAAACCACGACTCTCAGAAAAGGCAGCAGAGATGCTTCAGAACAAATATGTGGAGATTAGACAGgcacgtgctaaagatttttcacttagtctaactgttattaagact-gttctacttatttatttttt-----tcattgtgcag
















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|166453166|gb|EG266948.1|EG266948
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCG
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCG
EST: gi|76933303|gb|DV173407.1|DV173407
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|32824593|gb|CD964315.1|CD964315
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211443723|gb|FK945773.1|FK945773
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211443724|gb|FK945774.1|FK945774
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|76933305|gb|DV173408.1|DV173408
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211443722|gb|FK945772.1|FK945772
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211441602|gb|FK945769.1|FK945769
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211441601|gb|FK945768.1|FK945768
EST:     CGAGATTACACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211441600|gb|FK945767.1|FK945767
EST:     CGAGATTACACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|22546223|gb|BU098534.1|BU098534
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|71435361|gb|DR816411.1|DR816411
EST:     CAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|211441604|gb|FK945771.1|FK945771
EST:     CGAGATTACACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
EST: gi|71429881|gb|DR810931.1|DR810931
EST:     CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAG                         AAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC
genomic: CAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATC

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: 223

GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAA


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 36

GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 24

GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAA


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 15

GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctg ... tgttgcgcagAAAATGAGGCAGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACATTGAGTACTGCCGCGCCACATGCAAACCACGGCTTTCAGAAAAAGCAGCTGAGATGCTGCAGAACAAATATATCGAGATTAGACAGgtatacgctggatattttgacacaactagccggttttaagattcgttaaatgtgtttttagcttaaaatctgttgcgcag

- - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG