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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttcattgcaagagcattatgtctcatctgtctttatgtatagcagtgctggttaagtctgttttgattgagagttctaacaatcaaagttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG

Basic information

species Zea mays
transcript GRMZM2G160430_T01
intron # 10
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|5296357|gb|AI783127.1|AI783127
EST:     TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAAGAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
genomic: TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
EST: gi|148950294|gb|EC895853.2|EC895853
EST:     GGAATAAATTGTATAATCTTTTTAT-CAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGGT
genomic: GGAATAAATTGTATAATCTTTT-ATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGGT
EST: gi|32832825|gb|CD972503.1|CD972503
EST:     TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
genomic: TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
EST: gi|101387701|gb|EB815865.1|EB815865
EST:     AAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
genomic: AAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
EST: gi|32927095|gb|CF031907.1|CF031907
EST:     TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
genomic: TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
EST: gi|148950293|gb|EC895852.2|EC895852
EST:     TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
genomic: TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
EST: gi|5846979|gb|AW000058.1|AW000058
EST:     TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG                         GGCTCAAGAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
genomic: TGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG

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: 46 (upstream exon), 47 (downstream exon)
Score: 14

CTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 229

CTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 154

CTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 78

CTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAGgtaagctgtg ... agttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtgctggttaagtctgttttgattgagagttctaacaatcaaagttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG
                                ttctaac  putative branch site (score: 78)
                   ttttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttcattgcaagagcattatgtctcatctgtctttatgtatagcagtgctggttaagtctgttttgattgagagttctaacaatcaaagttctacagGGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - cattgca
- - - - - - - - - - - - - - - - - - -tatgtat
- - - - - - - - - - - - - - - - - - - - - - - - gtgctgg