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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctgctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG

Basic information

species Zea mays
transcript GRMZM2G118586_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112015_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g63090.3 (Oryza sativa), 3'ss of exon 1
gcctgctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG
                                |  ||  ||  ||||| ||||    |  |     |     |  | | | | |    |  | || | |||| ||||||||||| ||||| ||||| |||||  |||||||||||||||| || |||||||| |||
------------------------------tcagattatttgtggcgtttgctttggaagtatgggt----gagtgctcatgtgtttgtgctatt-gtaggctaatacgctgcgattgtatctcacttgcataagGAACACTCTGGAGGCTGCCATGTGCCTGCAG

upper sequence: GRMZM2G112015_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g63090.1 (Oryza sativa), 3'ss of exon 1
gcctgctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG
          | | || | | |    ||||  |  ||  ||  ||||| ||||    |  |     |     |  | | | | |    |  | || | |||| ||||||||||| ||||| ||||| |||||  |||||||||||||||| || |||||||| |||
---gttcgagattgcattttttttttaaaatcagattatttgtggcgtttgctttggaagtatgggt----gagtgctcatgtgtttgtgctatt-gtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG

upper sequence: GRMZM2G112015_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g63090.2 (Oryza sativa), 3'ss of exon 1
--gcctg---ctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG
  || |         | | || | | |    ||||  |  ||  ||  ||||| ||||    |  |     |     |  | | | | |    |  | || | |||| ||||||||||| ||||| ||||| |||||  |||||||||||||||| || |||||||| |||
tcgctttggttcgagattgcattttttttttaaaatcagattatttgtggcgtttgctttggaagtatgggt----gagtgctcatgtgtttgtgctatt-gtagGCTAATACGCTGCGATTGTATCTCACTTGCATAAGGAACACTCTGGAGGCTGCCATGTGCCTGCAG

upper sequence: GRMZM2G112015_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 1
gcctgctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttt-tcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG
|   ||||     | |  |     |  ||   ||| |   |||    |   ||| || | |     |   |  |  | |||   |   | ||   |  ||||| |||||| ||||||| ||| | |||||||| |||||||| || ||||| || ||||||||||||
gtacgctacgctcttatcaatcccctcaa-tcatcgtatcttc--tttacactaaactc-tgtttgtacaattatataaacacaccgtttttgcgtttcagGCAAATACGTTGCGGTTATACTTGACCTGCATTCGGAACACGCTCGAGGCCGCAATGTGCCTCCAG

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|85152679|gb|DW587816.1|DW587816
EST:     AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|32925177|gb|CF029989.1|CF029989
EST:     TGCCCAGGTCCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: TGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|21432169|gb|BQ547659.1|BQ547659
EST:     AGGTGCCCAGGTACTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|60346160|gb|DN213133.1|DN213133
EST:     TGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: TGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|211438327|gb|FL007592.1|FL007592
EST:     AGGTGCCCAGGTCCTCGTCCGGCCCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|32925995|gb|CF030807.1|CF030807
EST:     AGGTGCCCAGGTCCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|211435743|gb|FL007591.1|FL007591
EST:     AGGTGCCCAGGTCCTCGTCCGGCCCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
EST: gi|37376615|gb|CF624854.1|CF624854
EST:     AGGTGCCCAGGTCCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAG                         GCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG
genomic: AGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCG

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: 47 (upstream exon), 47 (downstream exon)
Score: 83

CTCTCTCCCTTCCGGCGACGCCTGGGCCACCGCCGCGGCCGCCCTACGCCAGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 103

CTCTCTCCCTTCCGGCGACGCCTGGGCCACCGCCGCGGCCGCCCTACGCCAGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

CTCTCTCCCTTCCGGCGACGCCTGGGCCACCGCCGCGGCCGCCCTACGCCAGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

CTCTCTCCCTTCCGGCGACGCCTGGGCCACCGCCGCGGCCGCCCTACGCCAGGTGCCCAGGTTCTCGTCCGGCTCTTCGCCGGCGATGAGCACCCACCAGgtatgccgac ... tttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG
                             cgttaac  putative branch site (score: 90)
                                          ctctttttcgc  putative PPT
                                           tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctgctataacttcagtatctggcaaaaactatcttcgtttcggcgtgtgctagacacatcgacatctcaaaacgttaacgagcgactctttttcgcagGCCAATACGCTGCGGTTGTACCTCACCTGCATCCGGAACACTCTGGAGGCGGCGATGTGCCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG