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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtagtgctacattcagcatcctcggccatgtttacgctttgctgcgaatcactcgttccgtttctgaagatcctaattaacttaacctttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG

Basic information

species Zea mays
transcript GRMZM2G020096_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 15
------------------------------gtagtagtgctacattcagcatcctc--ggccatgtt-tacgctttgctgcgaatca-----ctcgttccgtttct-gaagatcctaattaacttaacctttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG
                                | |  ||      ||| |||  ||  ||   || |   | ||      | ||| |      |   || ||||   ||  ||  |   || | ||  ||||| | |||||||||| || || ||||| || ||  || |||||||||||||||||||||||| ||| || | ||| ||| || | ||| |||||||||| ||   |  
gtgaagatttcaacattccagcatctcttttcattgatgaagatatcaacattttcatggttttgctgcgctctagataacaaatgaagaatttaactctgttttcagacaataattcgtagccta--ctttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAACGCAGCGTCGATCCTGTCTTCCAGGAGTTGTTATACTGATGCTGAGAAAC

upper sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 15
------------------------------gtagtagtgctacattcagcatcctc--ggccatgtttacgctt---tgctgcgaatcactcgttccgtt---tctgaagatcctaatt---aacttaacctttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG
                                | |  || |    | | |||  ||  ||   || |      |   |  |   ||| |   |||    |   | |  |||   |||||   | | ||  ||||| | |||||||||| || || ||||| || ||  || |||||||||||||||||||||||| ||| || | ||| ||| || | ||| |||||||||| ||   |  
gtgaagatttcaacattccagcatctcttttcattgatgatgatataaacattttcatggttttgctgggctctagataataaaaatgaagagtttaactctgttttcagacaataattcgtagccta--ctttgttgcagGAGTGACCCCAGCTGAGAGGCTGCTCAATTTGTACGAGACGAAGTGGCAACGCAGCGTCGATCCTGTCTTCCAGGAGTTGTTATACTGATGCTGAGAAAC
















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|26457119|gb|CA828702.1|CA828702
EST:     ACAAGGAGGCTCGGTTTCCTTAGAGAGGCTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ACAAGGAGG-TCGGTTTCCTTAGAGAGG-TTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|22543186|gb|BU093624.1|BU093624
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|113836047|gb|DW957174.1|DW957174
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTC
EST: gi|89251366|gb|DY623152.1|DY623152
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|78544507|gb|DV622005.1|DV622005
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTTTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|91048671|gb|EB159089.1|EB159089
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|211306279|gb|FL001392.1|FL001392
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|60345665|gb|DN212638.1|DN212638
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|166574970|gb|EG141182.1|EG141182
EST:     AAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
genomic: AAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC
EST: gi|18660951|gb|BM501134.1|BM501134
EST:     ATACAAGGAGGTCGGTTTCCTTAGAGANGTTGACGAAGTGGTGAGGACAG                         GAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAANTGGCAAC
genomic: ATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAAC

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: 204

AATGGATTGGAAAGAAGAGGATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 592

AATGGATTGGAAAGAAGAGGATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1489

AATGGATTGGAAAGAAGAGGATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

AATGGATTGGAAAGAAGAGGATACAAGGAGGTCGGTTTCCTTAGAGAGGTTGACGAAGTGGTGAGGACAGgtagtagtgc ... tttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgaatcactcgttccgtttctgaagatcctaattaacttaacctttgctacagGAGTGACACCTGCCGAGAGACTTCTGCATCTGTACGAGACGAAGTGGCAACGCAACGTAGACCATGTTTTCGAGCACTTGCTATACTGATGTTGTAGATG
                                           cctttgct  CT-rich tract
                               taattaacttaa  TA-rich tract