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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaaaacgcctctgttatccattgatttttttgacatgtctttcatggccgccaaggaaatattgtcagcattgtctttatatttagtttctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG

Basic information

species Zea mays
transcript GRMZM2G172322_T01
intron # 10
splice site 3'
intron type U2

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|149037276|gb|EE155319.2|EE155319
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|60359695|gb|DN226668.1|DN226668
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|211356738|gb|FL440505.1|FL440505
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|148956137|gb|EC901907.2|EC901907
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTTTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|149101004|gb|EE187101.2|EE187101
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|71319218|gb|DR796369.1|DR796369
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|76285084|gb|DV024652.1|DV024652
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|93017205|gb|EB642725.1|EB642725
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|211356737|gb|FL440504.1|FL440504
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|211428017|gb|FL465135.1|FL465135
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|211428077|gb|FL466325.1|FL466325
EST:     TYTAAAGATGAGGTTGTAAGTAAGCAGTAGATACCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGAACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|76932106|gb|DV172946.1|DV172946
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
EST: gi|60398346|gb|DN231162.1|DN231162
EST:     TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAG                         GTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA
genomic: TCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAA

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), 47 (downstream exon)
Score: 74

GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 99

GTAGAATCTAAAGATGAGGTTGTAAGTAAGCAGTAGATAGCATTTTTTCCTAGGAGgtaagcaatt ... tctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggccgccaaggaaatattgtcagcattgtctttatatttagtttctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG
                                           tttctgct  CT-rich tract
                          attgtctttatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaaaacgcctctgttatccattgatttttttgacatgtctttcatggccgccaaggaaatattgtcagcattgtctttatatttagtttctgctgcagGTGTTCTCGGGGGAGGGAGTATTCCTGCTGCAGGACGACAGCTGGACGGAATTTTGGAATACACCGGCAGAGTAGCTGAAATAACGGCTAGGAATTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
aagaaaa
- - - - gcctctg
- - - - - - - - - - - - - - - - tgacatg
- - - - - - - - - - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - gccgcca