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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttag

Basic information

species Zea mays
transcript GRMZM2G094051_T06
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 4
TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttag
||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||||||  ||| |   |    | || ||| || ||| |     ||    ||   | || | |||   | |     | |   |||| ||  |  ||
TATCAATGCCATGCACCCCAAGACCAGGAAGATCTTGCAGCTTCTGCGGTTGAGGCAGgttggtttatgaaccagttttcttagaaatgcgtgaactcttgcgtacgctggtgt-attaactttgtgcttaattgtttgatt-ctacag

upper sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 5'ss of exon 3
TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttag
||| || ||||||||||| |||||||||||||| ||||||||  |||| |||||||||||| ||    |  |  |  |  ||  |||     || ||  ||||| || | ||    |   |||   ||   ||  ||  |||  |  ||
TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtactgtcaattgaggaaa-aaatgttaattt--tgcag

upper sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 5'ss of exon 4
TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctg-attgtttgtaa---aactgaacatttgtttattttag-------
 || || || |||||||| |||||||||||||| ||||||||||| |||||||| |||||      | ||||   | |||||    || | ||   | | || |  | || |||  | |  || |||    ||  || |   |||| |  |         
GATCAATGCTATGCACCCGAAGACCAGGAAGATTTTGCAGCTTCTACGATTGAGACAGgtaaag--attgatacttttttttgtgttttctttttggtttttttgctcttttctttaataattataactggacaaaaaaaaagtttctgctgatggtttt

upper sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 4
lower sequence: EFJ23123 (Selaginella moellendorffii), 5'ss of exon 3
TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttag
||| |||| |||||| || |||||| ||||||||||||||||||| ||  || | |||||   ||| ||  ||   |||   |   |   |    | || |||  ||    |    |  ||| ||                        
TATCAACGACATGCATCCCAAGACCCGGAAGATCTTGCAGCTTCTTCGCCTGCGTCAGgtaaattc-cttgtgaaagttgcgattgtgatacgagttctcttactatcacattctttcttttatag-----------------------

upper sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 4
lower sequence: EFJ20182 (Selaginella moellendorffii), 5'ss of exon 3
TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttag
||| |||| |||||| || |||||| ||||||||||||||||||| ||  || | |||||   ||| ||  ||   | |   |   |   |    | || | |  ||   ||    |  ||| ||                        
TATCAACGACATGCATCCCAAGACCCGGAAGATCTTGCAGCTTCTTCGCCTGCGTCAGgtaaattc-cttgtgaaagctgcgattgtgaaacgagttctctgactatcacgttctttcttttatag-----------------------

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|211364904|gb|FL335329.1|FL335329
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAA
EST: gi|211197410|gb|FL309893.1|FL309893
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGAC
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGAC
EST: gi|211467480|gb|FL327940.1|FL327940
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTC
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTC
EST: gi|211430944|gb|FL367566.1|FL367566
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACWATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211331288|gb|FL346026.1|FL346026
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|76281808|gb|DV021376.1|DV021376
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211467080|gb|FL315617.1|FL315617
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACA
EST: gi|211425293|gb|FL350052.1|FL350052
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211419805|gb|FL340213.1|FL340213
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211489662|gb|FL352063.1|FL352063
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATT
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATT
EST: gi|31558661|gb|CD527873.1|CD527873
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGNGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211262500|gb|FL327821.1|FL327821
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211430817|gb|FL361882.1|FL361882
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGKGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211489013|gb|FL325724.1|FL325724
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
EST: gi|211427800|gb|FL348316.1|FL348316
EST:     CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG                         ATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA
genomic: CCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcac ... tttattttagATCTTCAATGGTGTGTTCCTCAAAGTCAACAAGGCGACTATTAACATGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAGgtgtgttcactgatgtctgtttttacaattgcattgctgctattataattttgtctgattgtttgtaaaactgaacatttgtttattttag

- - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - GCAGCT