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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttatgtcttgattgatatgcaattatttcatcatttctcgttgatgatgactgtaatttctgttagcttttggagtaatgaatataattgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 23
splice site 3'
intron type U2

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|32846872|gb|CD986553.1|CD986553
EST:     TGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: TGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|60345624|gb|DN212597.1|DN212597
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|32838986|gb|CD978667.1|CD978667
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|18963727|gb|BM660597.1|BM660597
EST:     ATGAGGAACCTGAAGTTGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|71443012|gb|DR824062.1|DR824062
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|67013339|gb|CO442088.1|CO442088
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|67016677|gb|CO445426.1|CO445426
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|6681776|gb|AW287763.1|AW287763
EST:     AAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: AAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|211347064|gb|FK984260.1|FK984260
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
EST: gi|60347180|gb|DN214153.1|DN214153
EST:     ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAG                         GCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA
genomic: ATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAA

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), 21 (downstream exon)
Score: 200

GTCAGGCATGATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG


Block sizes: 49 (upstream exon), 21 (downstream exon)
Score: 107

GTCAGGCATGATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG


Block sizes: 49 (upstream exon), 21 (downstream exon)
Score: 46

GTCAGGCATGATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG


Block sizes: 49 (upstream exon), 21 (downstream exon)
Score: 150

GTCAGGCATGATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatg ... ttgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgatgactgtaatttctgttagcttttggagtaatgaatataattgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG
 cgttgat  putative branch site (score: 150)
                                             ttgttctt  putative PPT
                                 taatgaatataattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttatgtcttgattgatatgcaattatttcatcatttctcgttgatgatgactgtaatttctgttagcttttggagtaatgaatataattgttcttagGCATCGGAAGAGAAGGAAATGCATAACACAGATGATGCTGATGAACATGAAGAGACAGTTTCAGTAAATGGGAACGAGGGTGAGGAACAGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - ttgattg
- - - - - - - - - tatgcaa
- - - - - - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttttg