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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttccaagcttacatcaactttcatactgcaacataccattgtagaaatgaaatgcgcccattttctgctctcatcctatgattccatttggatct...

Basic information

species Zea mays
transcript GRMZM2G460078_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 5'ss of exon 3
TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttccaag-cttacatcaac--tttcatactgcaacataccattgtagaaatgaaatgcgcccattttctgctctcatcctatgattccatttggatct
|||||| ||| |||||||||||||||||||||||||||||||||| || || || ||||||||||| |||||||| || |||||||||||||||||||| || ||||| ||  |||    ||    |||  |  ||||| | |      || | | ||||   |||    |||| || |||| |||     |  | |   |||
TGTTGCCGGGATATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTGCCTCTAGCACTTAGCTATCCTGAAGCTGAACTCCTTCATGTCATGAATGACTCGgtttgttctaaaacttgttgcagtgatttatttttgcaatagatgtacttacacaagaaagatgcca---ttctactatcatactacacacctctctctctct

upper sequence: GRMZM2G460078_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 5'ss of exon 3
TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttccaagcttacatcaactttcatactgcaacataccattgt--agaaatgaaatgcgcccattttctgctctc-atcctatgattccatttggatct
|||||||||  || | ||||| ||| ||  ||| || |||||||| || ||||| |||||||||||||||||||||||  | ||||| |||||||| || ||  |  |  |  ||||      ||   | ||   | ||   | |||  |  || | |    |  ||| ||  || ||   ||  ||  |    ||  ||   
TGTTGCTGGAATACTAGGAACTTGGTTTAGTGGAGGTGTTGCAGTTCCACTTGCACTTAGCTATCCAGAAGCTGAGCTCTTACATGTGATGAATGATTCGgttcgccctgaatttactctcttttattttcttgtatatttgagtgtttatgaaaggatccagttcatgtttagcactttgtctcatattgttgttgaga---
















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|78111750|gb|DV530147.1|DV530147
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|91049611|gb|EB160029.1|EB160029
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|211025828|gb|FK982703.1|FK982703
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCAC
EST: gi|211025826|gb|FK982701.1|FK982701
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|71434528|gb|DR815578.1|DR815578
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|71332183|gb|DR803010.1|DR803010
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|93012882|gb|EB638402.1|EB638402
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|148961982|gb|EE012780.2|EE012780
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|24766847|gb|CA401979.1|CA401979
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGGTGGGGGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|76925597|gb|DV170498.1|DV170498
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttccaagcttacatcaactttcatactgcaacataccattgtagaaatgaaatgcgcccattttctgctctcatcctatgattccatttggatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT