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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG

Basic information

species Zea mays
transcript GRMZM2G313649_T06
intron # 5
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|76294398|gb|DV033966.1|DV033966
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|71427980|gb|DR809030.1|DR809030
EST:     TTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|32942234|gb|CF047053.1|CF047053
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|32805213|gb|CD957449.1|CD957449
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTA
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTA
EST: gi|88748493|gb|DY532634.1|DY532634
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|71442372|gb|DR823422.1|DR823422
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|149084732|gb|EE174225.2|EE174225
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|71762245|gb|DR960182.1|DR960182
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|32789443|gb|CD941679.1|CD941679
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTA
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTA
EST: gi|88748628|gb|DY532769.1|DY532769
EST:     TAGGAAATGCCATTGGCAAACTGCATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|60343573|gb|DN210546.1|DN210546
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|32836689|gb|CD976367.1|CD976367
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc
EST: gi|213182702|gb|FM195363.1|FM195363
EST:     TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGAT                         TTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG
genomic: TAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTGgtgggtacaa ... atc

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), 45 (downstream exon)
Score: 91

TGGTTCAGATGGGGTCAATGAGGAACGCCTGAATGATATTGCCACACAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 53

TGGTTCAGATGGGGTCAATGAGGAACGCCTGAATGATATTGCCACACAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 111

TGGTTCAGATGGGGTCAATGAGGAACGCCTGAATGATATTGCCACACAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 65

TGGTTCAGATGGGGTCAATGAGGAACGCCTGAATGATATTGCCACACAAATAGGAAATGCCATTGGCAAACTACATGATGGAGGCCTTGTTCATGGTGATt ... tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tTTGACCACGTCAAACATGATAATTAAGAACAGTAACAATCAATTG

- - - - - - - - - - - -  AAGAAC