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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaactaggttcaacacttcaagatgaaagatctgcatgatgctaagctatgtgcattggtcccagtctctaacaatgcacattctgttttcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG

Basic information

species Zea mays
transcript GRMZM2G059381_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
taaactaggttcaacacttcaagatg-aaagatctgcatgatgctaagctatgtgcattggtcccagtctctaacaatgcacattctgttttctt-cttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG
 |   |   |  || | || || |    ||| | |   | ||  || |  || || |    ||  | |  |||          || |||| | ||  ||||||| | ||||||||||| || ||||||||||| ||||| || || ||||| ||  |||| ||||| || |||||||| ||||| || ||  | ||  | ||
cactttttatggaagaatttaaaagatgaagttatatttaat-ttatgtcatctgtagctttctta-tgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
-taaactaggttc-aacacttcaagatgaaagatctgcatgatgctaagctatgtgcattggtcccagt-ctctaacaatgcacattctgttttcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG
 | | ||   | |  || || | | |||| |  |  |  | ||    | |||  |       |   | | || |   | |  | || |  || | |  |||||| || || |||||||| |||||||||||||| ||||| || | |||||| ||  |||| ||||| || || ||||||||||| ||||| || ||    ||
gtgagctttttactgactctgcgatatgataagta-gagtaatttggaactaaatatccattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG
















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|213179260|gb|FM184509.1|FM184509
EST:     TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
genomic: TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
EST: gi|33090935|gb|CF050929.1|CF050929
EST:     TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
genomic: TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
EST: gi|87153602|gb|DY398391.1|DY398391
EST:     GATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
genomic: GATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
EST: gi|19350747|gb|BM895279.1|BM895279
EST:     AATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
genomic: AATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
EST: gi|58030032|gb|CX725459.1|CX725459
EST:     TATTGGCGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
genomic: TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
EST: gi|32847207|gb|CD986888.1|CD986888
EST:     ATCTCTAAATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAGC
genomic: ATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
EST: gi|211308069|gb|FL216534.1|FL216534
EST:     TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTG                         AGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC
genomic: TATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAAC

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: 45 (upstream exon), 49 (downstream exon)
Score: 166

CTTGAAGGGTATGGAATGACAGAGACATCTTGTGTCATCAGTACAATGAATATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 428

CTTGAAGGGTATGGAATGACAGAGACATCTTGTGTCATCAGTACAATGAATATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 184

CTTGAAGGGTATGGAATGACAGAGACATCTTGTGTCATCAGTACAATGAATATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 628

CTTGAAGGGTATGGAATGACAGAGACATCTTGTGTCATCAGTACAATGAATATTGGTGACAGATCAATTGGACATGTTGGATCTCCAAATCCTTCTTGTGgtaagctctg ... tcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctatgtgcattggtcccagtctctaacaatgcacattctgttttcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG
                      ctctaac  putative branch site (score: 628)
                                   cattctgttttcttct  putative PPT
                         taacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaactaggttcaacacttcaagatgaaagatctgcatgatgctaagctatgtgcattggtcccagtctctaacaatgcacattctgttttcttcttcagAGGTTAAACTTGTGGACGTCCCAGAAATGAATTATACTTCGGAGGATCAACCGTATCCTCGTGGAGAGATTTGTGTTAGGGGACCTATAATATTCTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA