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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacgtagttactaaggttattataatctgactctatttaccctctgtgtgtagtgggatgcccacttttctcagattcacttgtgtcttttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA

Basic information

species Zea mays
transcript GRMZM2G011219_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 3'ss of exon 12
-----gaacgtagttactaaggttattataatctgactctatttaccctctgtg--tgtagtgggatgcccacttttctcagattcacttgtgtcttttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA
          |   | |  |  |  |   || |      ||||| |  |  ||   | || | | ||  ||     || |   || |    | | ||       |||||  ||||||||||||||||| |   ||| ||||| |||||||| ||||| |||||||||||||| |||||||||||||||||| ||||||| |||||||
tccttctctattcattcccaattcgtagcaaacatgtgttattttcagttagttgctataatagaatagccttcactcccttgttaatacatatttt-------cagGGTACTGATCCAAGGCATGCACCACAAGACCAAGACCAAAGTTCCATGCTTAAGGTCATTTGCAATCAGAGGGATCGTTTCCGTACACGTCTACGTGAAA
















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|31359186|gb|CD443543.1|CD443543
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
EST: gi|67019074|gb|CO447823.1|CO447823
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
EST: gi|211487822|gb|FL394864.1|FL394864
EST:     TTGAATGACTGGGATATTCAAAGAAATCGGCTCAAGTTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCCGGCAGATCAAAGATCAAAGTTCGATGC
genomic: TTGAATGACTGGGATATTCAA-GAAATCGGCTCAAGT-GAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATC-GGCAGATCAA-GATCAAAGTTCGATGC
EST: gi|13382114|gb|BG458789.1|BG458789
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
EST: gi|60672578|gb|DN475280.1|DN475280
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
EST: gi|60399347|gb|DN232161.1|DN232161
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
EST: gi|211209479|gb|FL385673.1|FL385673
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC
EST: gi|8368393|gb|BE051338.1|BE051338
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAG
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAG
EST: gi|32928329|gb|CF033141.1|CF033141
EST:     TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCCGAG                         GGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTTGATGCTC
genomic: TCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTC

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), 47 (downstream exon)
Score: 194

GGCTACAGTTCAACTGATAGGAGGGGCTCACTCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

GGCTACAGTTCAACTGATAGGAGGGGCTCACTCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 154

GGCTACAGTTCAACTGATAGGAGGGGCTCACTCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GGCTACAGTTCAACTGATAGGAGGGGCTCACTCTTGAATGACTGGGATATTCAAGAAATCGGCTCAAGTGAAGCATCTGAGgtaatttcta ... ttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgtagtgggatgcccacttttctcagattcacttgtgtcttttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA
                                         tcttttattt  CT-rich tract
                                         tcttttattt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacgtagttactaaggttattataatctgactctatttaccctctgtgtgtagtgggatgcccacttttctcagattcacttgtgtcttttatttgcagGGCTCTGATCCAAGGCATGCATCGGCAGATCAAGATCAAAGTTCGATGCTCAAGGTCATTTGCAACCAGAGGGATCGTTTCCGTGCACGTCTGCGTGAAA

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