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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaggcaaacctggcaggcttgattaattgattcataaatagatgaggaccaacaacattttgctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG

Basic information

species Zea mays
transcript GRMZM2G070605_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 2
---------------------------------------gtaagta--ggcaaacctggcaggcttgattaattgattcataaatagatgaggacc-------aacaa-cattttgctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG
                                       || || |   |||| |   |    ||||  |      ||  ||  | | | | |||        ||||| | |  |||| | ||||||||||||||  ||||||||||  | || |||||||| ||||||||| | |||||||  ||||| ||||| ||||| |||
gtaagtgtattattgttcttccccccttgctttgcaacagtgagcatcagcaagctgcgtgatcttgcatt-ccattttgtagctgggttacgacatagtatgaacaatcgtactgcttgctgcagCTTTGTGTCGGTGATCCATCTGCTTGTTGGTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG
















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|149095141|gb|EE180755.2|EE180755
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|76914837|gb|DV165713.1|DV165713
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149013546|gb|EE043037.2|EE043037
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|101394747|gb|EB819306.1|EB819306
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|32925288|gb|CF030100.1|CF030100
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|148966890|gb|EE018012.2|EE018012
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149075192|gb|EE163691.2|EE163691
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|148986357|gb|EE030094.2|EE030094
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|211519067|gb|FL311546.1|FL311546
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149075125|gb|EE163618.2|EE163618
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|211407726|gb|FL367074.1|FL367074
EST:     ATATTCAACATCCTCAACAAGAGGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCCAGTAGTGGGGGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149112153|gb|EE191267.2|EE191267
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|32925201|gb|CF030013.1|CF030013
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|32924668|gb|CF029480.1|CF029480
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCAT
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCAT
EST: gi|91050012|gb|EB160430.1|EB160430
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149026859|gb|EE046212.2|EE046212
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149097452|gb|EE183315.2|EE183315
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|149015293|gb|EE045098.2|EE045098
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCCTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|71766326|gb|DR964263.1|DR964263
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|211475706|gb|FL352571.1|FL352571
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|78077772|gb|DV506204.1|DV506204
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
EST: gi|32925598|gb|CF030410.1|CF030410
EST:     ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA                         CTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG
genomic: ATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAG

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), 46 (downstream exon)
Score: 16

GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 586

GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 13

GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

GTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATAgtaagtaggc ... ctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgattaattgattcataaatagatgaggaccaacaacattttgctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG
                                        ttttgctc  CT-rich tract
     ttaattgattcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaggcaaacctggcaggcttgattaattgattcataaatagatgaggaccaacaacattttgctcgttgcagCTTTGTGTCCTTGATCCATCTAGTAGTGGGTGTCGTATACTGCCTCATCAGCTGGAGTGTCGGTCTCCCCAAGCGAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA