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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattatgaatcctatacaacttggtctgcattttctatttattcccatcgcgtgtgctttcattgtcatctttctgatgtgtgtcgccttcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC

Basic information

species Zea mays
transcript GRMZM2G180704_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|211185878|gb|FL440431.1|FL440431
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|148974738|gb|EE025549.2|EE025549
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|5871525|gb|AW017996.1|AW017996
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|60348073|gb|DN215046.1|DN215046
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|6095545|gb|AW120212.1|AW120212
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|6865264|gb|AW360614.1|AW360614
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|94477170|gb|EB706128.1|EB706128
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTTATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|166460037|gb|EG173169.1|EG173169
EST:     GCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: GCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|6031408|gb|AW076310.1|AW076310
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|60401527|gb|DN234334.1|DN234334
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|60339141|gb|DN206114.1|DN206114
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|116827763|gb|EC871704.1|EC871704
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|60400026|gb|DN232833.1|DN232833
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|5714045|gb|AI944030.1|AI944030
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAACAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|60352627|gb|DN219600.1|DN219600
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|76015666|gb|DT942836.1|DT942836
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|149088706|gb|EE177827.2|EE177827
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|6022259|gb|AW067187.1|AW067187
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|78022885|gb|DV491272.1|DV491272
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
EST: gi|94473980|gb|EB702938.1|EB702938
EST:     AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAG                         CTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT
genomic: AAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGT

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), 49 (downstream exon)
Score: 236

CTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTGAAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

CTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTGAAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

CTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTGAAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

CTTTCCTGCTCAAATTCATAACAATCATAACTTCAGTGCAGGGTCCATTGAAACTGATAGCCTGAGTGAGAGGTTAAGTTTAATTAAGTTTGAAATTCAGgtattttcat ... tcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcgcgtgtgctttcattgtcatctttctgatgtgtgtcgccttcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC
                           ttctgat  putative branch site (score: 174)
                                       tcgccttctt  putative PPT
             tttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattatgaatcctatacaacttggtctgcattttctatttattcccatcgcgtgtgctttcattgtcatctttctgatgtgtgtcgccttcttatgcagCTGTACAAAACAAGAGACGAGAAATACCTCCTCGATTTGCAAAGAGTCAGTGGGCCACAGCTCCTCTTTCTGGACTTGTGCGCGGCCTTTCTAACTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - tgaatcc
- - - - - - - atacaac
- - - - - - - - - - - - gtctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttc