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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctcttgttcctagatttttacttcctgggatgaactggtgtcattgagcaaatgtgtctgcactttcgggtggaagaataactttctgctgttt...

Basic information

species Zea mays
transcript GRMZM2G090722_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 1
TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggct-cttgttcctagatttttacttcctgggatgaactggtgtcattgagcaaatgtgtctgcactttcgggtggaagaataactttctgctgttt
||| |||||| |   ||||||| ||||| |||||||||||||||||||||||||| ||||||||||| || ||||||| ||| |||||||| ||| | ||||||  || ||| |   |   |||||  || ||        ||    |   |      |||  |  | | |     |   | ||| ||   | ||||| | 
TCCGCGTGCTGCAGCTCCTGCGGGAGCTCGGCTGCGGCGCCGTCCTCGTCAGCGGGAACGAGCTCCGCCTTGCCCTCCGGGCAGGATTCGATCCCACTAGgtgcatcttcttctcttttcgtttttcgtttctatctcccgctatatttgattttttgatggattggaattggaatgcaaatgaacaatgatttgctggt-
















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|149009813|gb|EE041699.2|EE041699
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|148944671|gb|EC889806.2|EC889806
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|149085087|gb|EE174595.2|EE174595
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|9731558|gb|BE510310.1|BE510310
EST:     GGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: GGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|148964387|gb|EC905763.2|EC905763
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|76017251|gb|DT944421.1|DT944421
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|50331439|gb|CO526565.1|CO526565
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|148941210|gb|EC886099.2|EC886099
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|148982703|gb|EE028519.2|EE028519
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|5268592|gb|AI770556.1|AI770556
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGG
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGG
EST: gi|6012246|gb|AW061788.1|AW061788
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GNGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|22473300|gb|BU037780.1|BU037780
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|87156171|gb|DY400960.1|DY400960
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|211304064|gb|FK992672.1|FK992672
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|30031720|gb|CB833571.1|CB833571
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTC
EST: gi|29167998|gb|CB411258.1|CB411258
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|149059656|gb|EE156999.2|EE156999
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
EST: gi|148940638|gb|EC885449.2|EC885449
EST:     AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAG                         GTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC
genomic: AGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGC

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 2 RNA-Seq libraries.


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 5

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGTGAATTTGATTTAGAGAAT


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 5

TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctct ... tgaagatcagGTGTATATTTAACGGAAATGGGAAGACACTCGAAGATCTTAAATTGGCTGCTGAGAGTGGAGTATTTGTAAATGTGGATAGTGAATTTGATTTAGAGAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCCGTGCTACGCGTCCTGCGTGAGCTTGGCTGCGGCGCCGTCCTCGTCAGCGGCAACGAGCTCCGACTCGCCCTCCAGGCGGGATTCGACCCCGCCAGgtgcggctcttgttcctagatttttacttcctgggatgaactggtgtcattgagcaaatgtgtctgcactttcgggtggaagaataactttctgctgttt

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