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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactttatctttagttatgatttggtataccttattttttggtgtcagatgatcattttgaccggccatacttcacgcag

Basic information

species Zea mays
transcript GRMZM2G015989_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 7
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactttatctttagttatgatttggtataccttattttttggtgtcagatgatcattttgaccggccatacttcacgcag
|| |||||||| |||||||||||||||||||||||||| || |||||||||||||| ||||| |||||||| |||||||| ||||||||||| |||||||||||  || | |||| |  || | |||      ||    | |  |   ||  ||  | | |  | ||  | |  ||||     
AACAGGCTTAGGGGTGCATTGAAGATTGCTGCTATTAAAGCTCCTGGTTTTGGAGAACGCAAGAGTCAATACCTTGATGATATTGCTACTCTTACTGGAGgtgatattcagcttttgacataagttg-----tctacactctaagccacacgtgcgcttatatatcgttcttctttcag----

upper sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 6
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgt------------gaactttat--ctttagttatgatttggtatacct-tattttttggtgtcagatgatc-----attttgaccggccatac-ttcacgcag-----------
|| |  ||||||||  || |||||||||| ||  | ||||||||||| |||||||||||||| || || || |||||||| ||||| |   | |||||||||             || || ||  ||||  || ||     |||||  |   ||||||  | ||   |  |      || ||||   |  ||   ||  | ||            
AACAAACTTAGAGGATCACTGAAGATTGCAGCACTGAAGGCCCCTGGGTTTGGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatataaaaatttcatgcctttgattttggaagtgtatatatgcttttttttctatctttttgtttccagatgttgataagatatgtattttctcaattggtttacag

upper sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 7
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactttatctttagttatga---tttggtataccttattttttggtgtcagatgatcattttgaccggccatactt-cacgcag
|| | |||||||||| || ||||||| || ||| | |  || || || |||||||||||||| || ||||| |||||||| ||||| | ||| ||||||||| |  | | |||  | | ||||    |  || |||     | ||||  ||       |  |  | |    | ||  |  |  ||||
AACAAGCTTAGAGGTACACTGAAGATAGCAGCTCTCAGAGCTCCAGGGTTTGGAGAGCGCAAGAGCCAATACCTTGATGATATTGCCATTCTAACTGGAGgtaagttctgtctgcattgatgagccctatgtttacgcatatatttgtagtttttatcttgtcctaattttctatcttcgcttgcag

upper sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 7
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactttatctttag----------ttatgatttggtataccttattttttggtgtcagatgatcat--tttgaccggccatacttcacgcag----------------------
|| | |||||||||  || |||||||||| ||| | || || ||||| |||||||||||||| || ||||| ||||| || ||||| | ||| |||||||||      | | ||||            |||   | |||||   | | | |    |      |    ||  |||| | |   | || | ||   |                      
AACAAGCTTAGAGGCACACTGAAGATTGCAGCTCTCAAAGCTCCTGGATTTGGAGAGCGCAAGAGCCAATACCTTGACGATATTGCCATTCTAACTGGAGgtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcag

upper sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 6
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactttatctttagttatgatttggtataccttattttttggtgtcagatga---tcattt-tgaccggccatacttcacgcag--------
|||| ||| || || ||||| |||||||||||  | || || ||||| ||||||||||||||||| |||||||||||||| |||||||  |||||||||||| |   |  |   |  | ||  ||| | ||    ||||   || |    | | |   |||| | | |      ||  || ||   |        
AATAAGCTCAGGGGGGCATTAAAGATTGCTGCACTGAAAGCTCCTGGATTTGGAGAGCGCAAAAGCCAATATCTTGATGATATTGCTATCCTCACTGGAGgttagtctatttagtgatgattgttttgcatctgctattgagtgtttcttgttaaaactcatgtataatacattat-ttttacttgggtattcag

upper sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 7
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactt---tatc--tttagttatgatttggtataccttattttttggtgtcagatgatcattttgaccggccatacttcacgcag------------
|||| |||||||||  |||| |||||||||||  |||| |||||||| |||||||||||||| || || || || ||||||||||| | ||| ||||||||| | | |   || |  |||   |||  |||  | | | |     |||  | | |  |||   ||||   |    || ||      |             
AATAAGCTTAGAGGGTCATTAAAGATTGCTGCACTTAAAGCCCCTGGATTTGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatagataacattttcactatttttttttcttcttctaaattttattttacttgagagttttattctaatattctgtcattattatatttgcaca

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|33093495|gb|CF053489.1|CF053489
EST:     TGGAGAGCGTAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32840618|gb|CD980299.1|CD980299
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32930585|gb|CF035397.1|CF035397
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCA
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCA
EST: gi|32935097|gb|CF039909.1|CF039909
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33093072|gb|CF053066.1|CF053066
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|67018624|gb|CO447373.1|CO447373
EST:     TGGAGAGCGCAAGAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|211161903|gb|FL325520.1|FL325520
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGASAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33099832|gb|CF059792.1|CF059792
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32840153|gb|CD979834.1|CD979834
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGGCATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32933116|gb|CF037928.1|CF037928
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAGGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33091567|gb|CF051561.1|CF051561
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32840911|gb|CD980592.1|CD980592
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32933836|gb|CF038648.1|CF038648
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33095277|gb|CF055271.1|CF055271
EST:     GAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: GAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32840280|gb|CD979961.1|CD979961
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32840621|gb|CD980302.1|CD980302
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GTACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32840609|gb|CD980290.1|CD980290
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33094337|gb|CF054331.1|CF054331
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32934585|gb|CF039397.1|CF039397
EST:     TGGAGAGCGTAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|67017327|gb|CO446076.1|CO446076
EST:     TGGAGAGCGCAAGAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAA-GCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|211451954|gb|FL157390.1|FL157390
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCASTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32841055|gb|CD980736.1|CD980736
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|78081967|gb|DV510379.1|DV510379
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|67022736|gb|CO451485.1|CO451485
EST:     TGGAGAGCGCAAGAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32936737|gb|CF041556.1|CF041556
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33100370|gb|CF060330.1|CF060330
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32841445|gb|CD981126.1|CD981126
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|33095378|gb|CF055372.1|CF055372
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
EST: gi|32841470|gb|CD981151.1|CD981151
EST:     TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAG                         GCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG
genomic: TGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaacttta ... cttcacgcagGCACTGTCATCAGAGAAGAAGTTGGATTATCCTTAGACAAGGCAGACAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAGGCTTAGAGGTGCATTGAAGATTGCTGCTATTAAGGCCCCTGGTTTTGGAGAGCGCAAAAGTCAATATCTTGATGACATTGCTACTCTCACTGGAGgtgaactttatctttagttatgatttggtataccttattttttggtgtcagatgatcattttgaccggccatacttcacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA