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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggatttatagacaatttatttctgcatggcatga...

Basic information

species Zea mays
transcript GRMZM2G139374_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 5'ss of exon 5
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgt-tttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggatttatagacaatttatttctgcatggcatga
||||| ||||| |||||| | |||| ||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| || |||| |   || |  | | | || | |   || |  |  |    | ||      ||  |   |    ||  | |  |||  |  |   || |
GTTGCCTCTGTGATGACTATGTGGAACAAACTTCAACCAGAGTATGCTGCCAACATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgtttcaattggcgcttgttatttgtttgattgtatttatttttcatggttcatcagcagctcagtgctctctgaagagtc-tttgggggttatatta

upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G45930.1 (Glycine max), 5'ss of exon 5
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggatttatagacaatttatttctgcatggcatga-------
|||||||  ||||||||  | |||||  | |||||||| || ||||| || ||||||||||| |||||| | |||||||| ||||||||||| || |||   ||| |  ||| | |   |  | | || | | | |   ||||          | |||   |       |  | ||||||||| ||   |  |       
GTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAAgtatgcggcaatcttgtttcttgctctaatac-agttatacacacataca------cacacacttgaaaaaggagaaataattatttctggatcagaaaatgtatta

upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA14G02820.1 (Glycine max), 5'ss of exon 5
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaat-ttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggattta--tagacaatttatttctgcatggcatga
|||||||  ||||||||  | |||||  | |||||||| || ||||| || ||||||||||| |||||| | |||||||| ||||||||||| || ||||  ||| |||||| ||| |         | |    | | || | |||      |    ||     ||    ||| ||| ||||  |   |   |   
GTTGCTTGCGTTATGACAATTTGGAGTCAACTTCAACCTGAATATGCAGCAAATATGTGGAATGAAGCCTTGAACAAACGACTTGGAACTAAAgtatgctgcaatcttgtttcttgctccaatacacacacccacacttgaaaaaggagaaataattttatttcttgatcagaaaatgtatta-taattaatac--

upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G27020.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctt---tggattta--tagacaatttatttctgcatggcatga
||||||||||| ||||| || ||||||||  | || || || ||||||||||| |||||||| |||||||||||||| || || |||||  |||| |    |  ||||||  ||  | ||||   |     |  | ||  |  | | ||| | | |||   |||||| |  ||   |     |||  |  | ||||  
GTTGCTTCTGTCATGACAGTTTGGAGCAAAATCCAGCCTGATTATGCTGCTAACATGTGGAATGAAGCCCTTAACAAGCGACTCGGAACAGAGgtattagcat-tttgttcatt--tatttcacttgttcataatgcttgatcaatcattttactcttctatggattaaaataagtagaaggttttagagtagcat--

upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ12449 (Selaginella moellendorffii), 5'ss of exon 5
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggatttatagacaatttatttctgcatggcatga
|| ||||| ||  | || || ||||     || ||||||||||||||||| ||||||||||| ||||| || ||||| || || |  ||| |||| ||  | | |||       | ||       | ||      | ||| || ||| ||  | |     |                                
GTGGCTTCGGTGCTCACGGTCTGGACTCGACTCCAACCAGAGTATGCTGCCAATATGTGGAATGAAGCTCTCAACAAGCGTCTCGACACTCAGgtatgacttagttt------cgatgagaaaagtggaaaa---cttgttcatgttttttgtgctaccag--------------------------------

upper sequence: GRMZM2G139374_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ34102 (Selaginella moellendorffii), 5'ss of exon 5
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggatttatagacaatttatttctgcatggcatga
|| ||||| ||  | || || ||||     || ||||||||||||||||| ||||||||||| ||||| || ||||| || || |  ||| |||| ||  | | ||||  |    |              ||  |  | |    | |||                                            
GTGGCTTCGGTGCTCACGGTCTGGACTCGACTCCAACCAGAGTATGCTGCCAATATGTGGAATGAAGCTCTCAACAAGCGTCTCGACACTCAGgtatgacttagtttggatgagagaagcggaaaactgggtcatgttttttgtgctatcag-----------------------------------------

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|6918323|gb|AW399853.1|AW399853
EST:     ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|148965947|gb|EE016863.2|EE016863
EST:     GCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: GCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|6637103|gb|AW261375.1|AW261375
EST:     GCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: GCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|71311669|gb|DR792242.1|DR792242
EST:     ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|148946743|gb|EC892009.2|EC892009
EST:     GAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: GAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|211364276|gb|FL199173.1|FL199173
EST:     ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|211364275|gb|FL199172.1|FL199172
EST:     ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
EST: gi|76011881|gb|DT939051.1|DT939051
EST:     ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAG                         GGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA
genomic: ATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaa ... ttattttcagGGTCTTGACCTTTCTGAAATCATAGTGGAATCAGAGAAACGTGGGATAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTTCTGTTATGACTGTATGGAGCAAGCTTCAACCAGAGTATGCTGCTAATATGTGGAAAGAAGCCCTTAACAAACGGCTTGGAACTAAGgtttgcttaaatttgttttttggtgtttctgctagatgttctcctgtacaagttattgttccctttggatttatagacaatttatttctgcatggcatga

- - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC