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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaagccacttgttgtgtagagtttaccagtgttgtatggagttcttttgtttgcaatcttctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 3'ss of exon 1
---agtaagccacttgttgtgtaga-gtttaccagtgttgtatggagttcttttgtttgcaatcttctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA
      ||  |      ||  |     |||   ||   ||   | | |   ||||||  |||| ||||  | || |   |     |||||| | ||   ||||||||||| || ||||||||||||||||||||||||||||||||||| ||||||   | ||| |||||||||| |||||||||||||||| | |||||||||
atgttgaattcgaaaaatgaatgattatttgatagaactgatagcattatgtttgttgacaattttctggtattaaacatc----atttctttttgcactccagGGGCAGCGCAATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAATGGTTGTCGGACACAGAAAATTATGTTATCAAGGGTTGTTTTTCCATGACAGAA

upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 1
agtaagccacttgttgtgtagagtttaccagtgttgtatggagttcttttgtttgc---aatcttctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA
   | | || ||||       |    |  | || || ||    |  |  || |  |    ||   ||||   ||| ||| |   ||   |  |||  || ||||||  | ||| | |||||||| ||||| |||||||| |||||||||||||||  | | || ||||| ||||||||||||||||||||||| ||| | || 
--catggcatttgtataaatcaagaaaagaatgatggatttgttcatgatgctaccttggattaactcactgttattttctctgatgaata-atggatttcagGGGTGGAGCCGTAAAGTTTCTGGGAACCAAGCGCCATCATGACAAGTGGTTGAATTCTACTGAAAACTATGATATCAAGGGTTGTTTTGCTATGTCTGAG

upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 1
agtaagccacttgttgtgtagagtttaccagtgttgt-atggagttcttttgtttgcaatctt-------ctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA
          || |||| |  |  | |  |      | ||||| || ||     | | | |||       ||||   ||| ||| |   ||   |  |||  || ||||||  | ||  | |||||||| ||||| |||||||| |||||||||||||||  | | || ||||| ||||||||||||||||||||||| ||| | || 
-------tttttcttgtttttaaatcaagaaaagaatgatggatttgttcacgataccaccttggattaactcactgttattttctctgatgaata-atggatttcagGGGTGGGGCAGTAAAGTTTCTGGGAACCAAGCGCCATCATGACAAGTGGTTGAATTCTACTGAAAACTATGATATCAAGGGTTGTTTTGCTATGTCGGAG

upper sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 1
----agtaagccacttgttgtgtagagtttaccagtgttgtatggagttcttttgttt--gcaatcttctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA
      || |  | |   | | || ||   |  | ||||||     | |     |||   | ||  |  | ||  |||| |  ||   ||  |  |||  || ||||||  |||||||| ||||| ||||||| ||||| || |||||||||||||||   | ||  || |||||||  ||||| ||||| |||||||||||||||
tcaatatatgttagtcagtat-taaagagaaaaattgttgtg----gctgcgaagttcaaggaacttgttaatcattaggtgctttc-ttcattgatgaatttcagGGGTGGTGCCATCCAGTTTTTTGGAACCAAGCGTCATCATGACAAGTGGTTGAGAGACAGTGAGAATTATGTGATCAAAGGTTGCTTTGCAATGACAGAA

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|211531376|gb|FL093845.1|FL093845
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534374|gb|FL093854.1|FL093854
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211306090|gb|FK992685.1|FK992685
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGNGTCCACTTNTTCCTCTG                         GGGNAGTGCCATCAAGTTTNTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|50322995|gb|CO518121.1|CO518121
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTCTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534377|gb|FL093857.1|FL093857
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|78118417|gb|DV536803.1|DV536803
EST:     CTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: CTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211306096|gb|FK992691.1|FK992691
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGAC
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGAC
EST: gi|211531379|gb|FL093848.1|FL093848
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534383|gb|FL093863.1|FL093863
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534378|gb|FL093858.1|FL093858
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|78122592|gb|DV540976.1|DV540976
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCCTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGAAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211531380|gb|FL093849.1|FL093849
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|6269967|gb|AW157938.1|AW157938
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211531373|gb|FL093842.1|FL093842
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211531377|gb|FL093846.1|FL093846
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211304074|gb|FK992682.1|FK992682
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211306088|gb|FK992683.1|FK992683
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTNCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGA-AAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211531369|gb|FL093838.1|FL093838
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211537384|gb|FL093868.1|FL093868
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534380|gb|FL093860.1|FL093860
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211537385|gb|FL093869.1|FL093869
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534371|gb|FL093851.1|FL093851
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211531381|gb|FL093850.1|FL093850
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|74241999|gb|DT649913.1|DT649913
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
EST: gi|211534385|gb|FL093865.1|FL093865
EST:     ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTG                         GGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT
genomic: ATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTT

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), 48 (downstream exon)
Score: 69

ACGGCGCTGCCGCCGAGCTCCGCAAACTAGCGCTCCTCGACTGCATCGCCATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 194

ACGGCGCTGCCGCCGAGCTCCGCAAACTAGCGCTCCTCGACTGCATCGCCATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

ACGGCGCTGCCGCCGAGCTCCGCAAACTAGCGCTCCTCGACTGCATCGCCATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

ACGGCGCTGCCGCCGAGCTCCGCAAACTAGCGCTCCTCGACTGCATCGCCATCTATGACCACTCTCTCGCCATCAAGATTGGCGTCCACTTCTTCCTCTGgtaatttttg ... tgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgtttgcaatcttctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA
                                     tttctctat  CT-rich tract
                       tttagtttattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaagccacttgttgtgtagagtttaccagtgttgtatggagttcttttgtttgcaatcttctcatgtttagtttattaaatttctctatgtgttccagGGGCAGTGCCATCAAGTTTCTTGGAACAAAGCGCCACCATGACAAGTGGTTGGTTGCCACGGAAAATTATGATATCAAGGGTTGTTTTGCAATGACAGAA

- - - - - ttgttgt
- - - - - - - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttt