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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactagacgatcacatgctgttaatggcatcaatcacatgcagcatatattctgccagatgcgcggtagttgtagctttcactgtttcattgcattcattgctgatgtttttgaatgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 16
----------------------------------gtaagtactagacgatcacatgctgttaatggcatcaatcacatgcagcatatattctgccagatgcgcggtag-ttgtagctttcactgtttcattgcattcattgctgatgtttttgaatgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC
                                   |   | | ||  | |||  |     ||     ||   | ||||    || |||||       ||   | || | |  || ||| || ||||| ||    ||| |   ||    ||| |||| | | | |||||||||||||||||||| |||||||| ||||||||||| || ||||||||||| ||||| |||||||| |||||||| |||||||||||||||||||||
gtgagaatatagcattactatacatttgacatttctttttgcgagtagctcaactagcagtatatttatatcttacatttttcacatattggcttttatttccagtgggtcataacttaca-tgttttataatgttcctaattggcacttt-gaataattatcagGACAAGTGTGGCTACACCAGAGCATGTTGAAGAGGCATTTAGGCTGTTCAATGTCTCCACTGTTGATGCCGCAAGATCTGGAATCAATGAGCATTTGAAC
















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|67015692|gb|CO444441.1|CO444441
EST:     CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|76933303|gb|DV173407.1|DV173407
EST:     CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|32824593|gb|CD964315.1|CD964315
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211443723|gb|FK945773.1|FK945773
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211443724|gb|FK945774.1|FK945774
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|76933305|gb|DV173408.1|DV173408
EST:     CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|78544713|gb|DV622211.1|DV622211
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211443722|gb|FK945772.1|FK945772
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211441602|gb|FK945769.1|FK945769
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211441601|gb|FK945768.1|FK945768
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211441600|gb|FK945767.1|FK945767
EST:     AGCTAGAAGCCATCATGCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: AGCTTGAAGCCATCAT-CCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|22546223|gb|BU098534.1|BU098534
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|71435361|gb|DR816411.1|DR816411
EST:     CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|211441604|gb|FK945771.1|FK945771
EST:     CAGCTAGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|71429881|gb|DR810931.1|DR810931
EST:     CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
EST: gi|149000776|gb|EE037999.2|EE037999
EST:     CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATT                         GACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA
genomic: CAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAA

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), 49 (downstream exon)
Score: 71

AGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC


Block sizes: 35 (upstream exon), 47 (downstream exon)
Score: 9

AGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 14

AGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC


Block sizes: 35 (upstream exon), 28 (downstream exon)
Score: 4

AGCAAGCTCACGAGACAGGGAGGGCCGCAGCTATACCCATCACAGTGAGGCAGCTTGAAGCCATCATCCGTTTGAGTGAATCTCTTGCAAAGATGAGATTgtaagtacta ... tgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagctttcactgtttcattgcattcattgctgatgtttttgaatgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC
                             tgctgat  putative branch site (score: 4)
                                                ctctt  putative PPT
                                     tttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactagacgatcacatgctgttaatggcatcaatcacatgcagcatatattctgccagatgcgcggtagttgtagctttcactgtttcattgcattcattgctgatgtttttgaatgactcttagGACAAGTGTGGCTACACCGGAGCATGTCGAAGAGGCATTCAGACTGTTCAATGTTTCCACCGTTGATGCTGCAAGATCCGGAATCAATGAGCATTTGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA