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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggatgtcacatgttttttgatagcatgccttaacatatactgctgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA

Basic information

species Zea mays
transcript GRMZM2G009021_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009021_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g46555.1 (Oryza sativa), 3'ss of exon 1
--ctggatgtcacatgttttttgatagcatgcct--taacat-atactgctgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA
  || ||| |      |  |   ||    |||||  |||  | |  ||| | | ||  |||||| ||| ||   ||||||| || ||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| || ||| ||||||| ||||||||||||||| || | || ||
tgcttgattttgtccctgctaccatttattgcctgataatgtgacgctgtttatgtactttaaa-tgagct---ttttttagca-tttcatttttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCATCCTCGACTGTGGTTGCGTGTTGAGAGGCCAATCAGAAATACAATAGA

upper sequence: GRMZM2G009021_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G54480.2 (Arabidopsis thaliana), 3'ss of exon 1
---ctggatgtcacatgttttttg-atagcatgccttaacatatactgctgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA
       || ||  || || |||| ||      | |   ||| |  |||  ||     |     | ||   | |||| | |  || || |||| ||   |||||||||||||||||| || |||||||||||||||||| | |  || || || ||||||||  | ||||| ||||| ||  |     |||  |||       |
tttgaaaatttcgtattttgtttgtatgattgacttgggcatttgttgcgtactacagtctgtttcaatgctgttttgtgt--atctc-ttgt-gagtttgcagATAGGTATAACACAGCACTCGTTTGCCACAGATGGAGATATCTGGCGTGTCACCCTCGCTTGTGGCTCCGTGTTGACCGTTTTGTCAAGGATTTATCTCA

upper sequence: GRMZM2G009021_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0139g00260.t01 (Vitis vinifera), 3'ss of exon 2
ctggatgtcacatgttttttgatagcatgccttaacatatactgctgacgtggtttaaaatga------actgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA
  |    |      |  |    | ||||    | | | ||  || || |        | ||||      || || | | | ||  ||| |    ||||   ||||||| |||||||||||||||||||||||||||||||||  | ||| ||||| ||||| || ||||||||||| || ||  || |  | | |||| |    ||
-agttcattctcgatactgctgttgcat---ctgagagatgttgttgccccatgcatatatgatatcatacagtctctgtcatggattgc--cattgagtttgcagATCGGTATAACACCGCCCTCGTTTGCCACAGATGGCATTACCTGGCATGTCACCCACGTCTATGGCTGCGAGTAGATCGGTCTGTGAAAGATTCATCTGA

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|211344537|gb|FL091805.1|FL091805
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342145|gb|FL091793.1|FL091793
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344534|gb|FL091802.1|FL091802
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342144|gb|FL091792.1|FL091792
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342151|gb|FL091799.1|FL091799
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342143|gb|FL091791.1|FL091791
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342152|gb|FL091800.1|FL091800
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342147|gb|FL091795.1|FL091795
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|30087498|gb|CB885704.1|CB885704
EST:     GCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGG-ATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|78121927|gb|DV540311.1|DV540311
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342146|gb|FL091794.1|FL091794
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344541|gb|FL091809.1|FL091809
EST:     GGACGACKGCTGCCTCATGCACATCTTCAGCTTCCTGAGCMCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342153|gb|FL091801.1|FL091801
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344538|gb|FL091806.1|FL091806
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211117409|gb|FL123096.1|FL123096
EST:     GGACGACRGCTGCCTCATGCACATCTTCAGCTTCCTGARCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344535|gb|FL091803.1|FL091803
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342149|gb|FL091797.1|FL091797
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCTCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344536|gb|FL091804.1|FL091804
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344543|gb|FL091811.1|FL091811
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344540|gb|FL091808.1|FL091808
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344542|gb|FL091810.1|FL091810
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211116627|gb|FL123094.1|FL123094
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342148|gb|FL091796.1|FL091796
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|29945972|gb|CB815913.1|CB815913
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211344539|gb|FL091807.1|FL091807
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
EST: gi|211342150|gb|FL091798.1|FL091798
EST:     GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAG                         ATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC
genomic: GGACGACGGCTGCCTCATGCACATCTTCAGCTTCCTGAGCCCAATCCCAGgttcgattcg ... gaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA
 tgctgac  putative branch site (score: 2)
        tttaaaatgaactgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggatgtcacatgttttttgatagcatgccttaacatatactgctgacgtggtttaaaatgaactgttttttttatcaatttcattgttgaacctgcagATAGGTATAACACCGCCCTCGTTTGCCACAGATGGCGCTTCCTTGCATGCCACCCTCGGCTATGGCTGCGTGTCGAGAGGCCAATCAGAGATGCGATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA