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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcaaagcagctcacatggatctccgcctgatcgaattcgttgagcaaagcagctcacatggatcaccgcctgatcgaatttctgctttgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 2
tgagcaaagcagctcacatggatctccgcctgatcgaattcgttgagcaaagcagctcacatggatcaccgcctgatcgaatttctg--ctttgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG
                 |   | |  |  | | |    ||   | | ||      ||  ||  ||||  |  |   || | | | ||  | ||| | ||||||| |  |||||||  |||||||||||||| || |||||||||||||| ||  |||||||||| ||||| ||||| |||||  | ||||| |  ||||| |
---------------gtacctacccacaacagctgcgcttgactcatcatcctcactt-cactgatcgtcatcaactcaactgtttgacccttgctgcacagCCTGACAAAGTCAAATTCCAACTAAGGCTGGGCCAGAGCAAGCCTATATACCAAGCTTTCAACGCCATAAGGAATTCTTCAGACTGGGAAACCCTCAGTG
















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|211451544|gb|FL256607.1|FL256607
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|149009256|gb|EE041351.2|EE041351
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|74240585|gb|DT648499.1|DT648499
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|211451543|gb|FL256606.1|FL256606
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|148950560|gb|EC896140.2|EC896140
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|211453674|gb|FL256610.1|FL256610
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|29544636|gb|CB605016.1|CB605016
EST:     CGTCAAGGACTCCCGCTGATCTCCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: CGTCAAGGACT-CCGCTGATCT-CCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|148960061|gb|EE153304.2|EE153304
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|149072691|gb|EE160926.2|EE160926
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|76020481|gb|DT947651.1|DT947651
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|211451546|gb|FL256609.1|FL256609
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|71437686|gb|DR818736.1|DR818736
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|148956895|gb|EC902819.2|EC902819
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|31354902|gb|CD439259.1|CD439259
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|148983362|gb|EE029348.2|EE029348
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
EST: gi|149075398|gb|EE163912.2|EE163912
EST:     AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAG                         CCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT
genomic: AGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTAT

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), 49 (downstream exon)
Score: 239

ACGCATCACCGACAGGCTCGAGGTGATCTGGGGCATGGTCGATCACCTCAAGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

ACGCATCACCGACAGGCTCGAGGTGATCTGGGGCATGGTCGATCACCTCAAGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

ACGCATCACCGACAGGCTCGAGGTGATCTGGGGCATGGTCGATCACCTCAAGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

ACGCATCACCGACAGGCTCGAGGTGATCTGGGGCATGGTCGATCACCTCAAGTCCGTCAAGGACTCCGCTGATCTCCGCGCCGCCGTAGAGGAAGTGCAGgttcacgatt ... tgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaaagcagctcacatggatcaccgcctgatcgaatttctgctttgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG
                                    tttctgctttgtttc  CT-rich tract
                                  aatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcaaagcagctcacatggatctccgcctgatcgaattcgttgagcaaagcagctcacatggatcaccgcctgatcgaatttctgctttgtttcacagCCCGTAAAAGTCAGTTTCCAACTAAGGCTAGGACAGAGCAAGCCTATCTATGAAGCTTTCAAGGCCATCAGGAACTCTTCTAATTGGGACAGTCTCAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-gagcaaa
- - - - gcagctc
- - - - - - - -acatgga
- - - - - - - - - - - - -ccgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccgcc