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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgattttgtctgttgtattttgtggaactactcattcgctatagacttgttagctatgtatccaggttttaatttggagacccatataccttct...

Basic information

species Zea mays
transcript GRMZM2G120115_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120115_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 5'ss of exon 4
CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgattttgtctgttgtattttg--tggaactactcattcgcta-tagacttgttagctatgtatccaggttttaatttggagacccatataccttct----------------------------------------------
||| ||||| || || |||||||||||||||||||||||||| ||||| ||||||  |||||||||||| ||||||| | |||||  |  || ||   || ||  | | |||| |  ||  | |  |    | | |  |||  |      ||  |||      ||  ||  ||    |                                              
CTATAACTCGAGCGAGGTGAACAATGGTGCTGATAAGTTGGCTGAGCAACGCACGGCGCTTCTAGAATCAAGAAGgtgaattgatagta-ctatttggttatgctttggactatttgttttcgaacatttctataaagtattcacttgttttgaaatgaatgaacaaattcactcctttgcaaatgtgtgaacatgataacctcaatttttttctttactgtag
















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|71444906|gb|DR825956.1|DR825956
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|33770632|gb|CF272926.1|CF272926
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|76290013|gb|DV029581.1|DV029581
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|60394595|gb|DN227465.1|DN227465
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|78108843|gb|DV527260.1|DV527260
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|18660756|gb|BM501031.1|BM501031
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|37392993|gb|CF633751.1|CF633751
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTTGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|88749057|gb|DY533198.1|DY533198
EST:     GATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|84977510|gb|DW475932.1|DW475932
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
EST: gi|50328759|gb|CO523885.1|CO523885
EST:     GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAG                         GCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT
genomic: GGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCAT

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: 141

CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCATTGAGGAGAGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCATTGAGGAGAGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCATTGAGGAGAGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgat ... tttaccatagGCAGGAGTTGGTCTTCTTGGACAATGAAATAGTGTTCAATGAGGCCATCATTGAGGAGAGGGATCAGGGAATACAAGAGATTCAACACCAAATCACTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAACTCAAGTGAAGTGAACAATGGTGCTGATAAGTTGGCAGAGCAGCGCACGCAGCTTCTAGAATCTAGAAGgtaagttgattttgtctgttgtattttgtggaactactcattcgctatagacttgttagctatgtatccaggttttaatttggagacccatataccttct

- - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT