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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat...

Basic information

species Zea mays
transcript GRMZM2G055905_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtc-ttcaaggatctgctagaagcattacac---acacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat
|||||||| || ||||||||||||||||||||||| ||||| ||||||||  ||||||||  |||||  |||||||||  || |   |||  |  ||| ||    ||   |||| | ||   | |   || ||||   || ||   |||  | || | ||   |   ||       
GTGTGGTCCGCTCCTAATTATTGCTACAGATGTGGAAATGTTGCTTCTATACTAAGCTTCAGTGAGACAATGgtatgtt-gtgcacctgtggtggaagcattatgtaattgcatcaaacttcatataggagtactag-gatttgctagtgcacttgtgcacacacaatacagag--

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G23310.1 (Glycine max), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattactt-ttgacttttgagtcaatttatacaataagtttatctcaat-
|| ||||||||||||||||| || ||| ||||||| ||||| ||||||||  | || ||| |||| || |||||  ||||  |||   |  ||      | |   |      || ||      ||||   || || |   ||  |||   | |||  |||  | | |     | 
GTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATGgtgagtca--tctgaagctttttgctgtgtttaaatctatttccatgataatgatggtttcttcatcatttggtcttgtgatatcatagttcttttcttttc

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G43470.1 (Glycine max), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattactt-ttgacttttgagtcaatttatacaataa-gtttatctcaat
|| ||||||||||||||||| || ||| ||||||| ||||| ||||||||  | || ||| |||| || |||||  ||||  |||   |  ||      | |  ||      || ||      ||||   || || | | ||  |||   | |||  ||   | || |||    
GTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATGgtgagtca--tctgaagctttttgctgtgttttaatctatttccatgataatgatggtttcttcattatttggtcttgtgatatcatggtgcttttcttttc

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G23310.4 (Glycine max), 5'ss of exon 8
----------------------------GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattactt-ttgacttttgagtcaatttatacaataagtttatctcaat-
                            || ||||||||||||||||| || ||| ||||||| ||||| ||||||||  | || ||| |||| || |||||  ||||  |||   |  ||      | |   |      || ||      ||||   || || |   ||  |||   | |||  |||  | | |     | 
AAGTCAATTCCCCTTTGGAAATTTGCAGGTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATGgtgagtca--tctgaagctttttgctgtgtttaaatctatttccatgataatgatggtttcttcatcatttggtcttgtgatatcatagttcttttcttttc

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G43480.1 (Glycine max), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcag--------ttcttttgtcttcaaggatctgctagaagcattacacacacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat-----------
|| ||||||||||||||||| || ||| ||||||| ||||| ||||||||  | || ||| |||| || |||||  ||||         || |  ||| || ||   | |         | |    |   ||   |  ||| | ||| |||    ||   | |  |   |||  ||  ||           
GTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATGgtgagtcaactgaaactttttgctgtgtttaaatctatatcgatgataatgatgatttcttcatcatttggtcttgtgatatcatg-gtgcttttcttttcccttgatgcatcaaatag

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G23310.3 (Glycine max), 5'ss of exon 9
-------------------------GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattactt-ttgacttttgagtcaatttatacaataagtttatctcaat-
                         || ||||||||||||||||| || ||| ||||||| ||||| ||||||||  | || ||| |||| || |||||  ||||  |||   |  ||      | |   |      || ||      ||||   || || |   ||  |||   | |||  |||  | | |     | 
TCAATTCCCCTTTGGAAATTTGCAGGTATGGTCTGCACCTAATTACTGTTACCGATGTGGAAATGTAGCTTCTATTCTGAGTTTCAATGAAAATATGgtgagtca--tctgaagctttttgctgtgtttaaatctatttccatgataatgatggtttcttcatcatttggtcttgtgatatcatagttcttttcttttc

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat--
||||||||||| |||||||| |||||| | ||||| ||||| |||||||| || || ||| |||| || |||||  | || || |||| ||||     |       |   || ||            | ||| | ||||||  |   | |  |      | | ||  |      
GTGTGGTCTGCGCCTAATTACTGCTACCGTTGTGGGAATGTGGCTTCTATATTGAGTTTCAATGACAACATGgtgaggcatttgttttctcttttgttactgatctgccacaatatcttgtttcatgttcttcttacttttatgc--actcgtcttcggattctacttttcctt

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttc-aaggatctgctagaagcattacacacacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat-
|| ||||||||||||||||| || ||| | ||||| |||||||||||||| || || ||| |||| || |||||  | |  |  |  | | | | ||     | ||  || | |  |   || |         ||  || ||   ||| |   |  ||| | ||  | | |   
GTATGGTCTGCACCTAATTACTGTTACCGCTGTGGGAATGTCGCTTCTATATTGAGTTTCAATGACAACATGgtgagcctctcttagtctttcctaaatgaatactctaatcttctctgtcagcaagaagggatt--ctattacttcagtgattttaatcatttcttttaagat

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgt--cagttcttttgtcttcaagg------atctgctagaagcattacacacacctga--ttacttttgacttttgagtcaatttatacaataagtttatctcaat--------------------------------------------------------
|||||||| || || || ||||||||||||||||| ||||| ||||| |||||||||||| | || || |||||| ||  ||  |||||    |||  |       |||       | ||||          |   ||| | ||   ||   |  | |  || | |  |  |  || ||||                                                         
GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATCTTAAGCTTCAACGAAAATATGgtaggtttcatatctttgacgttctggtcatgatatccaacgctatcattcttgttgttaggatttaatgttcctttgcaatgcgacgtacatatcacatgcatgtcaactgacattaatcaagttgacttctgatattgttactgatgtgattctgacatcgcag

upper sequence: GRMZM2G055905_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 5'ss of exon 9
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttctttt----gtcttcaaggatctgctagaagcattac---------acacacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat-----------------------------------------------------------------------------------
||||||||||| |||||||||||||| |||||||| ||||| ||||| || ||||||||| |||| || |||||| ||    | | ||    || | ||| | |    |   |  ||||          | |||  |  ||     |   ||   |  |||  | || | |   | | | |||                                                                                     
GTGTGGTCTGCTCCTAATTATTGCTATAGATGTGGAAATGTTGCTTCGATATTAAGCTTCAATGAAAATATGgtaggtttactgtgttacatgtatgcaatgcttattttatattattattttattttaaaacatgtatttggcaattttttgcaatgcaaagtgtatatttcatgtgtgtcagctaatatttattcttaagaagttatttatggaagctaggtttactttgcttcgttttgaagttcgcgtttatgttactttgcag

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|71302560|gb|DR787401.1|DR787401
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|71302558|gb|DR787400.1|DR787400
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|110223273|gb|EC905171.1|EC905171
EST:     GCTACAGATGTGGCAATGTCGCTTTTATTTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTTTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|76019063|gb|DT946233.1|DT946233
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|148947856|gb|EC893346.2|EC893346
EST:     GCTACAGATGTGGCAATGTCGCTTCTATTTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|71302302|gb|DR787269.1|DR787269
EST:     GCTACAGATGTGGCAATGTCGCTTTTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGGGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|76288840|gb|DV028408.1|DV028408
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|148941802|gb|EC886768.2|EC886768
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|16926550|gb|BM079618.1|BM079618
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|4630569|gb|AI621443.1|AI621443
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACATCCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|86468526|gb|DY234896.1|DY234896
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|148954451|gb|EC899875.2|EC899875
EST:     GATGAGAAGAGG                         GAAAGGGATGTCAAGTTTTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|211343234|gb|FL481284.1|FL481284
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|101381752|gb|EB812933.1|EB812933
EST:     GCTACAGATGTGGCAATGTCGCTTCTATTTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTTTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
EST: gi|60343653|gb|DN210626.1|DN210626
EST:     GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATG                         GAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA
genomic: GCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagt ... ctgttaccagGAAAGGGATGTCAAGTTCTTCACAGAGACAGAGGAGAACAACCAGATGCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTGGTCTGCACCTAATTATTGCTACAGATGTGGCAATGTCGCTTCTATCTTAAGCTTCGATGAGAAGATGgtatgtcagttcttttgtcttcaaggatctgctagaagcattacacacacctgattacttttgacttttgagtcaatttatacaataagtttatctcaat

- - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG