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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtttaattccatcccaaatttacagaatgcttctcaattataacacattaaggtatcttcctaaattttgttgcaaatgggtgactgacatgt...

Basic information

species Zea mays
transcript GRMZM2G178294_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178294_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g11200.1 (Oryza sativa), 5'ss of exon 13
ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtttaattccatcccaaatttacagaatgcttctcaattataac------acattaaggtatcttcctaaattttgttgcaaatgggtgactgacatgt
 |||||||| |||||||||||||||||||||||||||||||| ||  ||||||||||||||||||| || || || ||||||||||||||| | || |||||| ||    |  |  |   | ||| ||  ||| | | |||  |||  |||          | ||  ||||    ||||| || |  ||||   |   |       
TTATCCTGCGTATGGAACTTACGACTACAGCCATCAAATGCCTCAATCTGCTCCTCAAGCAGCTGCTTACGGCGCCTATCCTCCAACATACCCCGCTCAGgtactgaagatgttctccatctaaacttgtagagtacctctggatttgaactgctttgtgcttagtaatctgatcaaattgtgctcgaaattatt--ttag-----

upper sequence: GRMZM2G178294_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv07s0005g04290.t01 (Vitis vinifera), 5'ss of exon 9
ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtat---tgtgtttaattccatcccaaatttacagaatgcttctcaattataacacattaaggtatcttcctaaattttgttgcaaatgggtgactgacatgt
||||  ||  || ||||    | |   |  ||  ||||| ||     | |  || ||  | ||||| |||||||||||||||||||||||  |||  ||||||    ||   || ||| |||        |   |  |   ||   ||  | |   | |   ||  |     | |  || | |  | |       ||  |   
ATATAGTGGTTACGGAAGCAGCTATACCCACCCACAAATACCAACATCAGTGCCACAGACTGCTGCTTATGGTGCTTATCCTCCAACATATCCTGTTCAGgtaccagtggcatttattgcatttatttcctgtggtttcaatcctcatcctgattgacttcagttgcaaaaaataaattatggtgattttaattatgcta---
















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|32930152|gb|CF034964.1|CF034964
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|32933149|gb|CF037961.1|CF037961
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACANAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|32935217|gb|CF040029.1|CF040029
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|60350628|gb|DN217601.1|DN217601
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|32933726|gb|CF038538.1|CF038538
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACANAGCTACCCACAGCCTGCAGTAATTTCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|74245848|gb|DT653762.1|DT653762
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|60396359|gb|DN229228.1|DN229228
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|88747463|gb|DY531604.1|DY531604
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|211281773|gb|FL006153.1|FL006153
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCTTATACACAACAAAGCTACCCACAGCCTGCAGCAATTCTCAGCAGCACC
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTC-CAGCAGCACC
EST: gi|211283150|gb|FL440118.1|FL440118
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTYTGCACAG                         GCCTATACACAACAAAGCTACCCMCAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|44901202|gb|CK827747.1|CK827747
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCTTATACACAACAAAGCTACCCACAGCCTGCAGCAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|84969298|gb|DW467739.1|DW467739
EST:     CTCCTCAAGCAGCTGCTTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA
EST: gi|211420309|gb|FL467594.1|FL467594
EST:     CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAG                         GCTTATACACAACAAAGCTACCCACAGCCTGCAGCAATTCCAGCAGCACCA
genomic: CTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCA

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: 217

ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCAGTACCAGCACCTACAGCGCCGTCAGCTTATCCTCAACAACCTGCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCAGTACCAGCACCTACAGCGCCGTCAGCTTATCCTCAACAACCTGCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCAGTACCAGCACCTACAGCGCCGTCAGCTTATCCTCAACAACCTGCGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtt ... cttatcgtagGCCTATACACAACAAAGCTACCCACAGCCTGCAGTAATTCCAGCAGCACCAGTACCAGCACCTACAGCGCCGTCAGCTTATCCTCAACAACCTGCGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCCTGCATATGGAACTTACGACTACAGCCATCAAATGCCCCAGCCTGCTCCTCAAGCAGCTGCCTATGGTGCTTATCCTCCAACATACTCTGCACAGgtattgtgtttaattccatcccaaatttacagaatgcttctcaattataacacattaaggtatcttcctaaattttgttgcaaatgggtgactgacatgt

- - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC