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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataagatactactctgatattgcaaaatttactgtatattatttatatatggttgtgattattatttcctgaccattttcattctaccatgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG

Basic information

species Zea mays
transcript GRMZM2G314386_T01
intron # 1
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|211133492|gb|FL236781.1|FL236781
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGTACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|71442944|gb|DR823994.1|DR823994
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|149044645|gb|EE047617.2|EE047617
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|32837769|gb|CD977447.1|CD977447
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|148970703|gb|EE021421.2|EE021421
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|211311913|gb|FL092761.1|FL092761
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|74239171|gb|DT647085.1|DT647085
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|71449060|gb|DR830110.1|DR830110
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|211311911|gb|FL092759.1|FL092759
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCAKCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|148965413|gb|EE016213.2|EE016213
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|148933697|gb|EC877601.2|EC877601
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|211311912|gb|FL092760.1|FL092760
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|149073230|gb|EE161514.2|EE161514
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|32838159|gb|CD977837.1|CD977837
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAG-TGTTCTTCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|71442943|gb|DR823993.1|DR823993
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|211311910|gb|FL092758.1|FL092758
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCNAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
EST: gi|71775328|gb|DR973206.1|DR973206
EST:     TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCC                         AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC
genomic: TGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGC

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: 208

ACACTGGTTTGGCGCGAGACCATGGAGGGATCCCTGGAGGCGCGGCCCGGTGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 227

ACACTGGTTTGGCGCGAGACCATGGAGGGATCCCTGGAGGCGCGGCCCGGTGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 337

ACACTGGTTTGGCGCGAGACCATGGAGGGATCCCTGGAGGCGCGGCCCGGTGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 152

ACACTGGTTTGGCGCGAGACCATGGAGGGATCCCTGGAGGCGCGGCCCGGTGTCCTACTCGTCGGCGCCCCGGGCGTCGGCAAGCGGACCATCCTCTCCCgtgagatctc ... tgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatggttgtgattattatttcctgaccattttcattctaccatgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG
                      tcctgac  putative branch site (score: 152)
        ttgtgattattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataagatactactctgatattgcaaaatttactgtatattatttatatatggttgtgattattatttcctgaccattttcattctaccatgaactttagAGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG

- - - - - - - - - - - - - - tttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgac