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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatattgcgctgcatttcactagcatgaagcgtgttaacagttgtatcctttcccttgaactcgcggagcacgtttttgtaacagctttatctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC

Basic information

species Zea mays
transcript GRMZM2G160927_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 21
--------ttatattgcgctgcatttcactagcatgaagcgtgttaacagttgtatcctttcccttgaactcgcggagcacgtttttgtaacagctttatctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC
        | ||        | ||||     |  |     | || |   || | |    |  |  | ||| |  ||||  |   | |||      || || | | ||||| ||||||||||||||||| || || |||||||| ||||| ||||| || || |||| ||||||||||  ||| ||| | ||||||   |  |||||  
acggtctctaatgaaaaagagtattttttgggggtttgttgagtcaggggt-gcagatgtgactgt-aacaccaggagtgctaatatgt------ttcatgttttcagGCAAAGGAAGAGAAAGAGCTGCCTGAATACATTCTTGGCACAGTTCGCCTAAATCGTGCGAATCCCGACTCTGCAGTACCCATCTAAAGTCAGTTCTATA
















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|60397419|gb|DN230235.1|DN230235
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|32839402|gb|CD979083.1|CD979083
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTA
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTA
EST: gi|37394737|gb|CF634645.1|CF634645
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|32837394|gb|CD977072.1|CD977072
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGT
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGT
EST: gi|71439002|gb|DR820052.1|DR820052
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCT
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGA-GAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCT
EST: gi|211119644|gb|FL444181.1|FL444181
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|113826201|gb|DW946716.1|DW946716
EST:     GGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: GGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|60338548|gb|DN205521.1|DN205521
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|211043352|gb|FL434187.1|FL434187
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|33942624|gb|CF349224.1|CF349224
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|94476383|gb|EB705341.1|EB705341
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|8273067|gb|BE012162.1|BE012162
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTG
EST: gi|32935302|gb|CF040114.1|CF040114
EST:     TATTGGGATATGTCGCAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTAC
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTAC
EST: gi|32837391|gb|CD977069.1|CD977069
EST:     TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAG                         GCCAAGGAAGAGAAAGAGCTCCCCGAGTAC
genomic: TATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTAC

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: 203

AGATGTTGACATCGGTTCATCATCCGTTGCCCGGAGCATTATTGGTCTAGTATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 112

AGATGTTGACATCGGTTCATCATCCGTTGCCCGGAGCATTATTGGTCTAGTATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

AGATGTTGACATCGGTTCATCATCCGTTGCCCGGAGCATTATTGGTCTAGTATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

AGATGTTGACATCGGTTCATCATCCGTTGCCCGGAGCATTATTGGTCTAGTATTGGGATATGTCACAAGCATAGTTGTTGATCTTGCTATTCTTATTGAGgtactcccca ... atctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcctttcccttgaactcgcggagcacgtttttgtaacagctttatctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC
                                ttgtaac  putative branch site (score: 105)
                                         ctttatct  putative PPT
                             tttttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatattgcgctgcatttcactagcatgaagcgtgttaacagttgtatcctttcccttgaactcgcggagcacgtttttgtaacagctttatctgtgcagGCCAAGGAAGAGAAAGAGCTCCCCGAGTACATTCTGGGCACTGTTCGTCTGAACCGTGTGAATCCCGACAGTGCTGTATCAATCTAATTACGTTTCTAGC

- - - - -gctgcat
- - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttttg