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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcaaccatctccagctgccagtccgctcccctatggttaggttcatgctactggaaattctaatttttgtgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT

Basic information

species Zea mays
transcript GRMZM2G020418_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020418_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 1
gtaaggcaaccatctccagctgccagtccgctcccctatggttaggttcatgctactggaaattctaatttttgtgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT
||| |  ||||||||||  || | | |  | | |    || || ||||| |  |  ||  |   |||| |||||| |    ||| ||||||||||||||| |||||| ||||||||||||    || |||||||| ||||| ||||||||
gtaggcaaaccatctccctctccta-ttggtttcttggtgattcggttctttttgttgcga-ccctaaattttgtctcctctagGTACAAGGAGGATGTGTTGAACCCCAAGAAGAAGGATAACGAGAAGGAGAAGCTCGGGCGGAATGT
















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|33467366|gb|CF244415.1|CF244415
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCCATAA                         ATACAGGGAGGATGTGCTGAAC
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAAC
EST: gi|91876075|gb|EB406032.1|EB406032
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|76018426|gb|DT945596.1|DT945596
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|50332975|gb|CO528101.1|CO528101
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|76021688|gb|DT948858.1|DT948858
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|78077065|gb|DV505499.1|DV505499
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAAC
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAAC
EST: gi|74245267|gb|DT653181.1|DT653181
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|88752947|gb|DY537088.1|DY537088
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCANCA-GAAGAAGGACGTGGA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCA-CAAGAAGAAGGACGTGGA
EST: gi|50330327|gb|CO525453.1|CO525453
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|50326784|gb|CO521910.1|CO521910
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAG
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAG
EST: gi|211106067|gb|FL115242.1|FL115242
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         GTACAAGGAGGATGTGCTGAACCACAAGAAGAAGGA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGA
EST: gi|78087731|gb|DV516124.1|DV516124
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|93013576|gb|EB639096.1|EB639096
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|50326825|gb|CO521951.1|CO521951
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
EST: gi|148956652|gb|EC902508.2|EC902508
EST:     CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAA                         ATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA
genomic: CCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAA

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: 74

GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 28

GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 40

GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 45

GGTTTGGCTCGAGATGGGGAAGGCAAAGAGCAAGGGCCCTAAATTCGCGGCGGTGAAGAAGATTATCACCAAGAAAACCATCAATAAgtaaggcaac ... tgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcccctatggttaggttcatgctactggaaattctaatttttgtgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT
                                 ttctaat  putative branch site (score: 45)
                                       tttttgt  CT-rich tract
                              aaattctaatttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcaaccatctccagctgccagtccgctcccctatggttaggttcatgctactggaaattctaatttttgtgtatgatagATACAAGGAGGATGTGCTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA