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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgagtacgaatgattcagatacttaatcacttaagtggctacttcatgtgatgacgaagtactttatgtggtaacgattgtaccatttctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA

Basic information

species Zea mays
transcript GRMZM2G033526_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 1
-----ttttgagtacgaatgattcagatacttaatcacttaagtggctacttcatgtgatgacgaagtactttatgtggtaacgattgtaccatttctg-atgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA
     |  | | |    |   || | ||  |  |||| || | |    |  |  | |   ||   | ||    | ||||| |      | |  | | || |||||||  | |  | ||  |||   |||    ||||| || |  ||  |||| |||||  | || ||||||||||| || ||||||||||| |||||||||||||
acctctccttattcttgaatttttacattttccatcattttaat--tcagattgtcttccgatacaata----aagtggttagctcattcctttctttgcatgcagAACATTGCTGAGAATACCGCTGACGCTACTTCGCAAGTGGTCTCTGCGAATTCCCGTAGGAAGACAAAGATTGTTTGCACCATAGGCCCCTCAACCAACA
















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|211060146|gb|FL052188.1|FL052188
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|32823676|gb|CD963398.1|CD963398
EST:     GATCTCGCCGGCACGACCGACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: GATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|148969007|gb|EE019707.2|EE019707
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060152|gb|FL052194.1|FL052194
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|148931324|gb|EC874193.2|EC874193
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060145|gb|FL052187.1|FL052187
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211063106|gb|FL052207.1|FL052207
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211063103|gb|FL052204.1|FL052204
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|31348804|gb|CD433161.1|CD433161
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGTGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACATGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|33467027|gb|CF244076.1|CF244076
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060142|gb|FL052184.1|FL052184
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211254218|gb|FL052217.1|FL052217
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060143|gb|FL052185.1|FL052185
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060150|gb|FL052192.1|FL052192
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|32826166|gb|CD965844.1|CD965844
EST:     GATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: GATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211063109|gb|FL052210.1|FL052210
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|148955822|gb|EC901507.2|EC901507
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211063104|gb|FL052205.1|FL052205
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060141|gb|FL052183.1|FL052183
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211060148|gb|FL052190.1|FL052190
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
EST: gi|211478135|gb|FL462853.1|FL462853
EST:     CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGG                         ATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT
genomic: CGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAAT

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: 132

GCCTAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGGCGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

GCCTAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGGCGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

GCCTAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGGCGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 276

GCCTAGGAGGGCGGTGGCGGCGCAGTCGCTGCGGACGACCGCCACCGAGGCGCTGACGGCGGATCTCGCCGGCACGACCAACGGCGCTGTGCATGCTCGGgtgagtgcca ... tctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtgatgacgaagtactttatgtggtaacgattgtaccatttctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA
                                        ccatttct  CT-rich tract
                 tactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgagtacgaatgattcagatacttaatcacttaagtggctacttcatgtgatgacgaagtactttatgtggtaacgattgtaccatttctgatgcagATGAATAGTAAGGCTACAAGTGAAATCACTTCACAGGCAGTTACTGCAAATTCTAGGAGAAAGACAAAGATAGTCTGCACCATAGGTCCCTCAACCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - - - -tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtacca