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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatcggcatggttgcccccacagggctagttttccctcctttttttctttcactttgcaccactaccccccagctgttcccaatatgttttcac...

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 8
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|211193716|gb|FL465420.1|FL465420
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|32165106|gb|CD670424.1|CD670424
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTGCTTCTTGAG                         ATATATGCGCCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|149077066|gb|EE165722.2|EE165722
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|71767590|gb|DR965527.1|DR965527
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|110965155|gb|EE185055.1|EE185055
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|37392565|gb|CF633534.1|CF633534
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|211190973|gb|FL452316.1|FL452316
EST:     CAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: CAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|31909789|gb|CD651094.1|CD651094
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|148938717|gb|EC883049.2|EC883049
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|67020721|gb|CO449470.1|CO449470
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|37381267|gb|CF627509.1|CF627509
EST:     GAATCTGGATCTAATAG-TTTTGNATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: GAATCTGGATCTAATAGTTTTTG-ATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|148974380|gb|EE025157.2|EE025157
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|76285047|gb|DV024615.1|DV024615
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|67013918|gb|CO442667.1|CO442667
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|211193717|gb|FL465421.1|FL465421
EST:     AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
EST: gi|78105578|gb|DV523996.1|DV523996
EST:     AGAATCTGGATTTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG                         ATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC
genomic: AGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAAC

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: 153

AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAA


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

AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 168

AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatc ... ttggatgaagATATATGCACCATGGTGTGGTCATTGTCAATCGCTGGAACCTACTTACAACAATCTAGCCAAGCATCTACGTAGTGTTGACTCCCTTGTGGTAGCCAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAGgtatgacatcggcatggttgcccccacagggctagttttccctcctttttttctttcactttgcaccactaccccccagctgttcccaatatgttttcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccca