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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCATCGCCGGCGCCGATTACTGTGTCGTCGCGGCGGACACCCGCCTCTCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccctgaacccgatctcgtgcttcgatctgtccatctgggctttagggtttgtggattgggaggcacgagtgaattttggtgtggcgtgggctaa...

Basic information

species Zea mays
transcript GRMZM2G074386_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074386_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 2
TGGCCATCGCCGGCGCCGATTACTGTGTCGTCGCGGCGGACACCCGCCTCTCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccctgaacccgatctcgtgcttcgatctgtccatctgggctttagggtttgtggattgggaggcacgagtgaattt-tggtgtggc-gtgggctaa
|||||||||||||||| || ||||| || || || || || |||||||| || |||||||||| ||||||||||||||||||||| ||||||||||| |||| |||||| |  ||  ||| ||  |  ||||||| ||   | ||  ||||||||||| ||||||||||   | |||  ||| || || |   | | |   |
TGGCCATCGCCGGCGCGGACTACTGCGTGGTGGCCGCCGATACCCGCCTTTCCGTCGGATACAACATCCTCACGCGCGACCACTCCAAGATCTGCGAGCTgtaagtcccgg--ccgaatcgcggcccccgatctgcccgctttgggcttagggtttgttgattgggagggctgtgtgggtttgtgatgcgcttgggagtcga
















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|211293899|gb|FL244459.1|FL244459
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211423761|gb|FL057574.1|FL057574
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211304832|gb|FL260605.1|FL260605
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211293903|gb|FL244463.1|FL244463
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151431|gb|FL260598.1|FL260598
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211304831|gb|FL260604.1|FL260604
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211399896|gb|FL244532.1|FL244532
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211300322|gb|FL244507.1|FL244507
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211149988|gb|FL260580.1|FL260580
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151434|gb|FL260601.1|FL260601
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211302466|gb|FL244528.1|FL244528
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151420|gb|FL260587.1|FL260587
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151421|gb|FL260588.1|FL260588
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211289625|gb|FL244438.1|FL244438
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211293906|gb|FL244466.1|FL244466
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211302460|gb|FL244522.1|FL244522
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151427|gb|FL260594.1|FL260594
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211149990|gb|FL260582.1|FL260582
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211149983|gb|FL260575.1|FL260575
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151422|gb|FL260589.1|FL260589
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGGCTGACAAATGTGTACTAGCATCTTCTGGNTTTCAGGGTGATATTAAAG
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGG-CTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAG
EST: gi|211300327|gb|FL244512.1|FL244512
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|116819555|gb|EC862690.1|EC862690
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211151428|gb|FL260595.1|FL260595
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GNCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|32910464|gb|CF015276.1|CF015276
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAGGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
EST: gi|211149994|gb|FL260586.1|FL260586
EST:     TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCT                         GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC
genomic: TCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGC

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: 291

TGGCCATCGCCGGCGCCGATTACTGTGTCGTCGCGGCGGACACCCGCCTCTCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

TGGCCATCGCCGGCGCCGATTACTGTGTCGTCGCGGCGGACACCCGCCTCTCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

TGGCCATCGCCGGCGCCGATTACTGTGTCGTCGCGGCGGACACCCGCCTCTCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 261

TGGCCATCGCCGGCGCCGATTACTGTGTCGTCGCGGCGGACACCCGCCTCTCTGTCGGATACAGCATCCTCACGCGCGACCACTCTAAGATCTGCGACCTgtgagtccct ... ttatgtgtagGGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG