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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttctaaatggcatacgtattacttcaaagaaatgaagaaaaaatgatcataccattctgtgtgatatggtgagacaatgagcttttataatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG

Basic information

species Zea mays
transcript GRMZM2G128491_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128491_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g27010.1 (Oryza sativa), 3'ss of exon 3
tccttctaaatggcatacgtattacttcaaagaaatgaagaaaaaatgatcataccattctgtgtgatatggtgagacaatgagcttttataa--tctgcag-
  |      || |  ||   || ||||      | || |  | |   ||| |  ||||  ||   ||||||| ||   ||  |  |||| |||  |||||||         |  ||||| ||  | ||| |  |||| || |  |||||| |||  ||| |||| |||||||||| ||| |||| ||||||||||||||||          
-gcagtagtattgtcta-acatgacttaggtttactgcattacatcagatgaatccataatgaacgatatggagattaaagcattttttttaatatctgcagCCAGTTACTGTGAGCCACATTTCATTTGCTGAGGATGGAAGTGTTCCTCCCAAAAAGCCAACTTCAGTGGCTGAGGTAGCAAAGCAGCGTGAGCTTAGCG---------
















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|87157807|gb|DY402596.1|DY402596
EST:     AGGCCGAGAGCGCCGCCGCCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: AGGCCGAGA--------G-CGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|76287576|gb|DV027144.1|DV027144
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|71307158|gb|DR789750.1|DR789750
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|148956639|gb|EC902493.2|EC902493
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|9254985|gb|BE345453.1|BE345453
EST:     AGGCCGAGAGCGCCGCCGCCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: AGGCCGAGA--------G-CGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|78114333|gb|DV532722.1|DV532722
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|12968693|gb|BG265639.1|BG265639
EST:     GTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGCCA
genomic: GTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|71430885|gb|DR811935.1|DR811935
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|211018202|gb|FL215892.1|FL215892
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|78118764|gb|DV537148.1|DV537148
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|211015418|gb|FL215877.1|FL215877
EST:     GGATATCNAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|211018200|gb|FL215890.1|FL215890
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|22715254|gb|BU197664.1|BU197664
EST:     AAGG-CGAGAGCGCCGCCGCCGCCNCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: AAGGCCGAGA-----G-CGCCG--TCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|211018199|gb|FL215889.1|FL215889
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|22819528|gb|BU499618.1|BU499618
EST:     AGGCCGAGAGCGCCGCCGCCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: AGGCCGAGA--------G-CGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|76936903|gb|DV174954.1|DV174954
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|71327882|gb|DR800570.1|DR800570
EST:     GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAG                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
EST: gi|211018201|gb|FL215891.1|FL215891
EST:     GGATATCCAAGGCCGANAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAR                         GCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA
genomic: GGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCA

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), 48 (downstream exon)
Score: 112

GAAGACGGGCTCCTCGCCCAAGGGGAAGGAGACAACAGGGACCGGGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG


Block sizes: 38 (upstream exon), 47 (downstream exon)
Score: 32

GAAGACGGGCTCCTCGCCCAAGGGGAAGGAGACAACAGGGACCGGGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 18

GAAGACGGGCTCCTCGCCCAAGGGGAAGGAGACAACAGGGACCGGGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 152

GAAGACGGGCTCCTCGCCCAAGGGGAAGGAGACAACAGGGACCGGGATATCCAAGGCCGAGAGCGCCGTCGCAACTGCCTCCCGTGATCGTCAGgtgcacaact ... taatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatcataccattctgtgtgatatggtgagacaatgagcttttataatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG
                                       cttttat  CT-rich tract
                                        ttttataatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttctaaatggcatacgtattacttcaaagaaatgaagaaaaaatgatcataccattctgtgtgatatggtgagacaatgagcttttataatctgcagGCTAGCCAGATCACCTTTTCCCAGGACGGGACCGTTCCTACCAGGAAGGCAACCTCAGTGGCTGGGGTGGCAAGGCAGCGTGAGCTTAGCCATACCGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - -ggcatac
- - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - aaaaaat