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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTACCCTTGGTTGATCCTTCATCAGCTTTATGTGATAATCAATTCAATGATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatttgttccctttttcgtttgtattagtcgacgttatttatgttctaccttctttaattattgtacctcttttgtccacaatag

Basic information

species Zea mays
transcript GRMZM2G093096_T01
intron # 4
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|166477073|gb|EG149180.1|EG149180
EST:     ATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAG                         ATATACCAAGAGGATTTGATGGAGTTGTTGCCCA
genomic: ATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCA
EST: gi|67026168|gb|CO454917.1|CO454917
EST:     ATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAG                         ATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGC
genomic: ATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGC
EST: gi|67039995|gb|CO466250.1|CO466250
EST:     ATACCTACCTGTTCAGTGAACCAAAGAATGTGAATGCATATGGGGAACAG                         ATATACCAAGAGGATTTGATGGAGTTGTTCCCC-CTGACCAGATATGCCGC
genomic: ATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGC
EST: gi|67041729|gb|CO467984.1|CO467984
EST:     ATACCTACCTGTTCCCCGAACAAAAGAATGTGAATGCATATGGTGAACAG                         ATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGC
genomic: ATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGC

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), 49 (downstream exon)
Score: 218

ACTACCCTTGGTTGATCCTTCATCAGCTTTATGTGATAATCAATTCAATGATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGCGGACATGAAAACATTGATATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

ACTACCCTTGGTTGATCCTTCATCAGCTTTATGTGATAATCAATTCAATGATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGCGGACATGAAAACATTGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

ACTACCCTTGGTTGATCCTTCATCAGCTTTATGTGATAATCAATTCAATGATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGCGGACATGAAAACATTGATATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

ACTACCCTTGGTTGATCCTTCATCAGCTTTATGTGATAATCAATTCAATGATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatt ... tccacaatagATATACCAAGAGGATTTGATGGAGTTGTTGCCCACTGACCAGATATGCAGCGGACATGAAAACATTGATATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTACCCTTGGTTGATCCTTCATCAGCTTTATGTGATAATCAATTCAATGATACCTACCTGTTCAGTGAACAAAAGAATGTGAATGCATATGGTGAACAGgcaagtcatttgttccctttttcgtttgtattagtcgacgttatttatgttctaccttctttaattattgtacctcttttgtccacaatag

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