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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttattagctccaagtacttcagttgtttctactgtaaatggttgttgctcagtatgattctctgtatatttgtag

Basic information

species Zea mays
transcript GRMZM2G047855_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 8
GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttattagctccaagtacttcagttgtttctactgtaa-atggttgttgctcagtatgattctctgtatatttgtag
||||||||||||||| ||||| || ||||| |||||||||||||||||||||||||| |||||||||||| | | ||||    |  |||       || ||  ||| ||  |  ||||| |  || || || |||| ||||||||
GCATAGTAGAAAACCATGGTCGAAATTCATTAATGCTGATAACCAACATCTAGTATCTCCTGAGgtttgtcaatggctcttgctgtttc---caaatcaaccttaagataatgtttgcttaacatcatgct-tgtacatttgtag

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S165_119V6.3 (Physcomitrella patens), 5'ss of exon 8
------------------------------------GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttattagctccaagtacttcagttgtttc--tactgtaaat-----ggttgttgctcagtatgattctc-tgtatat--ttgtag-----------------------------------------------------------
                                    |||||| || ||||| |||||||||||||| ||||||||||| || ||||| ||    || ||||| ||| |   | |   |  | ||   | | ||   ||   | |||     | || | | ||   ||| || ||  | |||   | ||                                                             
TGACGTCTCTTACTACTGTGTTGTTGGTTCCTTCAGGCATAGCAGGAAACCTTGGTCAAAGTTCATCAATGCTGATAATCAGCATCTGGTTGTTCCAGAGgtatgtgaa-ggttttgaaaatttggttagattgcgtatcatcaatcatttgcttctggttctacatgtttttcacgcataccatcgtgagtcttcgtgttcaacattttgtttatattaatgaaagagtaaattgttattttctgcag

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 9
GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttattagctccaagtacttcagttgtttc--tactgtaaat-----ggttgttgctcagtatgattctc-tgtatat--ttgtag-----------------------------------------------------------
|||||| || ||||| |||||||||||||| ||||||||||| || ||||| ||    || ||||| ||| |   | |   |  | ||   | | ||   ||   | |||     | || | | ||   ||| || ||  | |||   | ||                                                             
GCATAGCAGGAAACCTTGGTCAAAGTTCATCAATGCTGATAATCAGCATCTGGTTGTTCCAGAGgtatgtgaa-ggttttgaaaatttggttagattgcgtatcatcaatcatttgcttctggttctacatgtttttcacgcataccatcgtgagtcttcgtgttcaacattttgtttatattaatgaaagagtaaattgttattttctgcag

upper sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 5'ss of exon 8
GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttattagctccaagtacttcagttgtttctactgtaaatggttgttgctcagtatgattctctgtatatttgtag---------------------
 |||||||| ||||| |||||||| ||||| |||||||| ||||||||||| ||  | || ||||| |||    |  | |  | | | |   ||    ||||   ||||  | || ||   ||   || ||   | | |  ||                      
ACATAGTAGGAAACCTTGGTCAAAATTCATAAATGCTGACAACCAACATCTGGTTGCTCCGGAGgtatgtgtcaattttctggaagtgctagtgaaattacttacaatgtat-tttctacatacctttttcacaaaaatattaatctattaactggttaggtttc

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|67025945|gb|CO454694.1|CO454694
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         -CCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|71761092|gb|DR959029.1|DR959029
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|6095381|gb|AW120048.1|AW120048
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|149085357|gb|EE174864.2|EE174864
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|37388000|gb|CF631204.1|CF631204
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|31998439|gb|CD662075.1|CD662075
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|149097606|gb|EE183499.2|EE183499
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|32925527|gb|CF030339.1|CF030339
EST:     AACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: AACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|31997697|gb|CD661720.1|CD661720
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|60345677|gb|DN212650.1|DN212650
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|32839753|gb|CD979434.1|CD979434
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGC
EST: gi|5607774|gb|AI901441.1|AI901441
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|32925412|gb|CF030224.1|CF030224
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGA
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGA
EST: gi|7216891|gb|AW563013.1|AW563013
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|71446426|gb|DR827476.1|DR827476
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|5525642|gb|AI861535.1|AI861535
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|110941068|gb|EE161225.1|EE161225
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|30705895|gb|CD058961.1|CD058961
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|14203981|gb|BG837658.1|BG837658
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|60340774|gb|DN207747.1|DN207747
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|7227707|gb|AW566348.1|AW566348
EST:     CAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCGCCAAGATAGGCTC
genomic: CAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|30706066|gb|CD059017.1|CD059017
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|148929900|gb|EE285653.2|EE285653
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|5922209|gb|AW055479.1|AW055479
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCACCATCTAGTATCNCCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCCCCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|32870873|gb|CF010555.1|CF010555
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|149109954|gb|EE293763.2|EE293763
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|30087041|gb|CB885249.1|CB885249
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|7135281|gb|AW498007.1|AW498007
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|18177159|gb|BM378369.1|BM378369
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|67020854|gb|CO449603.1|CO449603
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|19436338|gb|BM952748.1|BM952748
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
EST: gi|6095382|gb|AW120049.1|AW120049
EST:     CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAG                         GCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC
genomic: CCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTC

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), 46 (downstream exon)
Score: 339

GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 367

GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 381

GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttatt ... atatttgtagGCCATAGATTTTCTCGATAAGCTCCTGCGCTATGATCACCAAGATAGGCTCACTGCACGTGAAGCTATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATAGTAGAAAACCCTGGTCAAAGTTCATGAATGCTGATAACCAACATCTAGTATCACCTGAGgtttgttattagctccaagtacttcagttgtttctactgtaaatggttgttgctcagtatgattctctgtatatttgtag

- - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - GCTGAT