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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggaggacggtctttccctcttcggacgagtattacatttggtttctgtgaatggttcatttcacattagtgtaacatatgtcatgatctttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA

Basic information

species Zea mays
transcript GRMZM2G055520_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055520_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g06070.1 (Oryza sativa), 3'ss of exon 10
caggaggacggtctttccctcttcggacgagtattacatttggtttctgtgaatggttcatttcacattagtgtaacatatgtcatg-----atctttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA
            ||| | || | |  |  | |||||  |||  | | || ||||| || ||| ||| || ||| |||||||| |||       |  || || |||||||||||||| |||||||| |||||||||||||| ||||| || || || ||||| |||||||| || ||||| ||||| || ||| | || |||||||
--------gtaacttgctctatgcatatta-tattaatttttatatgtgagaatgatttattgcacgtttgtg-aacatatggcatttttatgttctttttgcagCCTCTTCCTACTAAGCTAGTATTGCAGAAGAAAAAAGCAAAAGAAGGCAGATCTGGGGATGAAATTGAGCATTTCCCAGTGCCCTCCAGGATTACTGTGA
















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|67028367|gb|CO457116.1|CO457116
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|211117417|gb|FL123104.1|FL123104
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|6445442|gb|AW179360.1|AW179360
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|5108209|gb|AI739922.1|AI739922
EST:     CCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|6342626|gb|AW165450.1|AW165450
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|78026209|gb|DV494596.1|DV494596
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|51592768|gb|CV071914.1|CV071914
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|12973657|gb|BG268590.1|BG268590
EST:     CTCCAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|6445422|gb|AW179490.1|AW179490
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|71432829|gb|DR813879.1|DR813879
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|76286686|gb|DV026254.1|DV026254
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
EST: gi|101389744|gb|EB816806.1|EB816806
EST:     CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG                         CCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG
genomic: CTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGG

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: 74

GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 100

GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 51

GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTGgtaattagtg ... tttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgaatggttcatttcacattagtgtaacatatgtcatgatctttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA
                         gtgtaac  putative branch site (score: 51)
                                           tctttatttc  putative PPT
                                          atctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggaggacggtctttccctcttcggacgagtattacatttggtttctgtgaatggttcatttcacattagtgtaacatatgtcatgatctttatttcagCCTCTTCCTACCAAGCTAGTTTTGCAGAAGAAAAAGGCAAAGGAGGGGAGGTCTGGAGATGAAATCGAACATTTTCCAGTACCTTCCCGTATCACTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - tacattt
- - - - - - - - - - - - - - - - - - - - - - - - gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgatc