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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactttgtgataggtgacataaagatccaatgttgtatgcaagtttccccagttacatcaaactattttgtggtcttagtcttttctaacagtag...

Basic information

species Zea mays
transcript GRMZM2G083546_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083546_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 5'ss of exon 4
AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAA---CGCCTCAAAAGCTCAGgta----------caaactttgtgataggtgacataaagatccaatgttgtatgcaagtttccccagttacatcaaactattttgtggtcttagtcttttctaacagtag
    || || ||||||||||||||||||||  ||||||| |||||||| || |||| |||||| |||||||||||| ||||||     ||| ||||  | ||||||          |||  |||||| || || | ||||  |   |||    ||       ||  |   |  ||  | |  | ||||     ||    || | | |      
---TGGCCACGTAGCACCACCAAAATCATCAAACTTCTTTCAAGAGTACGGAATGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattgaaccaatgtttgtgctatgtca-ataagtaaataataa-atagattgacttttctgat--caatacataagtttgcaaagtttactttctatga------
















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|148994701|gb|EE034198.2|EE034198
EST:     GGAGGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTTTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|32837598|gb|CD977276.1|CD977276
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCCAAT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGC-AAT
EST: gi|78092043|gb|DV520417.1|DV520417
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|88746794|gb|DY530935.1|DY530935
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGTTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|1498115|gb|AA030725.1|AA030725
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|149086706|gb|EE176245.2|EE176245
EST:     CAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: CAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|60358412|gb|DN225385.1|DN225385
EST:     CGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: CGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|6022125|gb|AW067053.1|AW067053
EST:     TCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGGAACTGAT-AAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: TCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|109179344|gb|EC379938.1|EC379938
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|37381689|gb|CF627745.1|CF627745
EST:     CAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: CAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|74237116|gb|DT645030.1|DT645030
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|60342316|gb|DN209289.1|DN209289
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|78024255|gb|DV492642.1|DV492642
EST:     GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: GGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
EST: gi|60355340|gb|DN222313.1|DN222313
EST:     AGAAATCAAGCAACGCCTCAAAAGCTCAG                         ATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT
genomic: AGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATT

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: 47 (upstream exon), 49 (downstream exon)
Score: 182

AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATTTCGTCATCTCAGTTTTTTGGTACTCAAAACAGAGAAGAGAAAGAGGCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 269

AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATTTCGTCATCTCAGTTTTTTGGTACTCAAAACAGAGAAGAGAAAGAGGCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 329

AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATTTCGTCATCTCAGTTTTTTGGTACTCAAAACAGAGAAGAGAAAGAGGCTC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 387

AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactt ... ttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATTTCGTCATCTCAGTTTTTTGGTACTCAAAACAGAGAAGAGAAAGAGGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCGGTCATGTAGCACCACCAAAATCATCTGACTTCTTCCAAGAGTATGGGATGGGTAATGGATTCCAAAAGAAATCAAGCAACGCCTCAAAAGCTCAGgtacaaactttgtgataggtgacataaagatccaatgttgtatgcaagtttccccagttacatcaaactattttgtggtcttagtcttttctaacagtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA