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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaatttttaagcatttcttaacgatattgtttggaatatgaagctcatataatcctttagcttgatttataattagatacttccaggcatcagcttattttgtgtacatatttgcag

Basic information

species Zea mays
transcript GRMZM2G114758_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114758_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g09920.2 (Oryza sativa), 5'ss of exon 7
TACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaatttttaagcatttcttaacgatattgtttggaatatgaagctcatataatcctttagcttgatttataattagat-acttccaggcatcagcttattttgtgtacatatttgcag
| ||||||||||| || ||||| ||||| || ||||| || ||||||||| |||| ||||||||||||||||||||||||||||||||||||||| | |  ||| |||| | || ||      |  | |  |    | || ||| | ||| |       |||| |||| | | || | ||  ||| |  |  |   || |||        
TGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaaatctccagcctttccttacaat------taaactgagctattaatttaaacttttggacca---tatagttagtttagtttctggattcatcgcagct---gttcatg-------

upper sequence: GRMZM2G114758_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT5G10070.1 (Arabidopsis thaliana), 5'ss of exon 7
TACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaatttttaagcatttcttaacgatattgtttggaatatgaagctcatataatcctttagcttgatttataattagatacttccaggcatcagcttattttgtgtacatatttgcag
|||||||||| |||||||| ||||| || || |||||  | ||||||||  | ||||||||||| |||||||| || ||  | ||| |||||| | |    | ||| |  |    | |    |  |  | |     || |   || | ||| |  | ||| ||||    |||| | |    |   |  ||                   
TACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATGgtgagtccataacatcttctcctaaaacccatccgtctcttctattcgtc--atacattatccggttttctaatgtcttact-ctatctgttttccaatcag----------------

upper sequence: GRMZM2G114758_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0031g01200.t01 (Vitis vinifera), 5'ss of exon 7
TACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaatttttaagcatttcttaacgatattgtttggaatatgaagctcata-taatcctttagcttgatttataattagatacttccaggcatcagcttattttgtgtacatatttgcag
|||||||| |||| |||||||| || || || ||||| || |||||||| || || ||||||||||| ||||| |||||  |  | ||||||||     ||  | |  |||  | || ||   |  | |   | ||| ||  || |||| |    || ||| | || |     ||  |  ||  | |||   | |||             
TACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATGgta-ccagtattcttgacttttc-atgtttcatctattcgaatgcttatgctattcctattagatggtttgtgatca-----ttgtaatcactatcttgcatagtgc------------

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|12972397|gb|BG267961.1|BG267961
EST:     TGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: TGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|110193278|gb|EC875176.1|EC875176
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|78544567|gb|DV622065.1|DV622065
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCACATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|86468292|gb|DY234662.1|DY234662
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|83279425|gb|DV943433.1|DV943433
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|94473540|gb|EB702498.1|EB702498
EST:     TTATCAGCAGCCCTCATAATATG                         TGGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTC
genomic: TTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagT-GGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTC
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|60345140|gb|DN212113.1|DN212113
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|78074927|gb|DV503361.1|DV503361
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|78118561|gb|DV536945.1|DV536945
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|89251519|gb|DY623305.1|DY623305
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|213167931|gb|FM194811.1|FM194811
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAANNNNGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
EST: gi|211480276|gb|FL093313.1|FL093313
EST:     CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG                         TGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA
genomic: CCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaattttta ... atatttgcagTGGGGAGGAAGATACAGCGCATTTGCTGCTTGGGAAATTTAAATGGGGTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATGgtaatttttaagcatttcttaacgatattgtttggaatatgaagctcatataatcctttagcttgatttataattagatacttccaggcatcagcttattttgtgtacatatttgcag

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