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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttatcttggcccttgaacgtaaacgaggatgcctttccgctgtcaatctcatgcaccctggcttttagcaaggatgtccaaaattagatgaatgctctttacttagctgtgttcaagatggacaatcaatgattttgatctttttccctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTCAATGTTTTTTTCTCACTAGTTTCTAAATGGTACAAGAGCGATAAACTGG

Basic information

species Zea mays
transcript GRMZM2G005308_T02
intron # 12
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|211462206|gb|FL207483.1|FL207483
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|211459691|gb|FL207478.1|FL207478
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|24769907|gb|CA405036.1|CA405036
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGCCAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|211183290|gb|FL434310.1|FL434310
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|60394413|gb|DN227283.1|DN227283
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|71764578|gb|DR962515.1|DR962515
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|71761969|gb|DR959906.1|DR959906
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|211183291|gb|FL434311.1|FL434311
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|31364214|gb|CD448569.1|CD448569
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|76011806|gb|DT938976.1|DT938976
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|60353438|gb|DN220411.1|DN220411
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|40303495|gb|CK347882.1|CK347882
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
EST: gi|37392792|gb|CF633649.1|CF633649
EST:     ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAG                         CATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC
genomic: ACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTC

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), 46 (downstream exon)
Score: 12

GAAGAGATATTTGAAGGAAAAGGTGATGTTAAGGAAGAGGGGGAACTTACACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTCAATGTTTTTTTCTCACTAGTTTCTAAATGGTACAAGAGCGATAAACTGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 20

GAAGAGATATTTGAAGGAAAAGGTGATGTTAAGGAAGAGGGGGAACTTACACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTCAATGTTTTTTTCTCACTAGTTTCTAAATGGTACAAGAGCGATAAACTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 19

GAAGAGATATTTGAAGGAAAAGGTGATGTTAAGGAAGAGGGGGAACTTACACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTCAATGTTTTTTTCTCACTAGTTTCTAAATGGTACAAGAGCGATAAACTGG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 20

GAAGAGATATTTGAAGGAAAAGGTGATGTTAAGGAAGAGGGGGAACTTACACAGGCTGAGCGCAAGAGAAGAAGAGCTAACAAGAAAAGGAGATATGCAGgtaattttta ... cctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTCAATGTTTTTTTCTCACTAGTTTCTAAATGGTACAAGAGCGATAAACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagctgtgttcaagatggacaatcaatgattttgatctttttccctaatgcagCATCCCATAAGGAGAGGACAGCGCCAGCCAAGTTGCAGAAAGATTAAACTCAATGTTTTTTTCTCACTAGTTTCTAAATGGTACAAGAGCGATAAACTGG
                                            ccctaat  putative branch site (score: 20)
                               ttttgatctttttccc  CT-rich tract
                              attttgatcttttt  TA-rich tract