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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccccccctcccttgtattatatgccctatatatgtatatgttactttttgttctacaattgtagtttggtgcgaccgtttattttttactcaa...

Basic information

species Zea mays
transcript GRMZM2G017086_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 9
TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccccccctcccttgtattatatgccc-tatatatgtatatgttactttttgttctacaattgtagtttggtgcgaccgtttattttttactcaa--
|||| || | |||  ||  |||||| |||| |||||||| ||||||||||||||||||| || | | ||| ||  | | | |  | |  | | |   | |       |  | |  |  |||||  |   |||| |  | ||| | || |||  |   
TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAGCAGgttctctctctctctctctc-tctcacacacacacacacacacacacacacactcatctgttttaattggggg--ggtgtgttcttttctgttgtacaaaggt
















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|32934266|gb|CF039078.1|CF039078
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32826398|gb|CD966076.1|CD966076
EST:     GATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: GATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|241994792|gb|GR421145.1|GR421145
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCGCTGTGCANAAAGTGGTGAGGAGAGCATGGAGACAGAATCAG
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAG
EST: gi|32803651|gb|CD955887.1|CD955887
EST:     GATC-CGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: GATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32932531|gb|CF037343.1|CF037343
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGTAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|211437528|gb|FK975648.1|FK975648
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32863109|gb|CF002791.1|CF002791
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32930082|gb|CF034894.1|CF034894
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32945380|gb|CF050199.1|CF050199
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32866635|gb|CF006317.1|CF006317
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32911302|gb|CF016114.1|CF016114
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|32932473|gb|CF037285.1|CF037285
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGTAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|74240015|gb|DT647929.1|DT647929
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAG
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAG
EST: gi|32931528|gb|CF036340.1|CF036340
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGACCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|67017287|gb|CO446036.1|CO446036
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATA
EST: gi|50332356|gb|CO527482.1|CO527482
EST:     TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAG                         GGTCCACTGTGCAGAAA
genomic: TCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAA

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: 48 (upstream exon), 48 (downstream exon)
Score: 165

TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccc ... ttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATCTGCAGCTCTTCCGATGAAGCAACTATTTGGGATAGATCTCGTGAGCAGgttctgtccccccctcccttgtattatatgccctatatatgtatatgttactttttgttctacaattgtagtttggtgcgaccgtttattttttactcaa

- -  CTGCAG
- - -  GCAGCT
- - - - CAGCTC
- - - - - - - - - - TGAAGC
- - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc