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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatcgtcgcttttttccttaatacgaaacaaagtgcccattatgcaaattatgtttttttaatttagcaactgaactttatatttgacttacaa...

Basic information

species Zea mays
transcript GRMZM2G042992_T01
intron # 21
splice site 5'
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|76280738|gb|DV020306.1|DV020306
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
EST: gi|76934579|gb|DV173944.1|DV173944
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
EST: gi|211316878|gb|FL253814.1|FL253814
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
EST: gi|89761150|gb|DY689280.1|DY689280
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
EST: gi|89764406|gb|DY691228.1|DY691228
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
EST: gi|76929334|gb|DV171965.1|DV171965
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTTCAAA-GTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGT-CAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTT
EST: gi|5499066|gb|AI854933.1|AI854933
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGA
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGA
EST: gi|89764424|gb|DY691240.1|DY691240
EST:     TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGAT                         GTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT
genomic: TTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTT

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), 48 (downstream exon)
Score: 389

TGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

TGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatc ... cttacatcagGTCAAAAGTAAGCTCAAGGGACATCAGAAGAAGATTACGGGGCTGGCCTTTTCTCAATCAATGAATGTGCTAGTATCATCAGGTGCTGATGCTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCAACTTTCCTTGCATTCCACCCACAAGATAATAATATCATCGCCATTGGAATGGAGGACTCTACCATCCAAATCTACAATGTCCGCATTGATGATgtatgctatcgtcgcttttttccttaatacgaaacaaagtgcccattatgcaaattatgtttttttaatttagcaactgaactttatatttgacttacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacaaa