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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtttctacatctttgtacttaaaagtgtttgtttggatattagttttagtatatttttttgaagcaacactttatgtttctataga...

Basic information

species Zea mays
transcript GRMZM2G030280_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 5
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtttctacatctttgtacttaaaagtgtttgtttggatattagtttt-agtatatttttttgaagcaacactttatgtttct-ataga--
||||||||||| || || |||||||| ||||||||||||||||| ||  | ||||| ||||||  ||| || |     ||  | ||||     ||||   |||| ||    |   |||||| |  ||   |  || |  | |   | ||| ||| | ||     
ACATTGCGTCGGCTCGCCCAAAATCGCGAGGCTGCAAGGAAGAGTCGTTTGAGGAAAAAGgtacttgtgttctg----ctgtagcttttatactaaagaagtttattccttttcaagttttgaaaattgatggtttataccatgttctatttttttcattctgt

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 7
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtt---tctacat---ctttgtacttaaaagtg------tttgtttggatattagttttagtatatttttttgaagcaacactttatgtt--tctataga--------------------------------------------
|||||  | || ||||||||||||||||||||||| ||||| |||||||| ||||| |||||| |    |||  |||   | || ||   ||| | |  | |  |||       ||| || | | ||   | |   ||||| ||  ||  |||||  ||||  |  | |||| |                                            
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttctgttaattttagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattgagacccaacaacttatcatgttttataaatatttctgaacttcttttttaaatccttgtttctattcattcag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G31050.3 (Glycine max), 5'ss of exon 7
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagttt-ctacatctttgtacttaaaagtgtttgtttggatattagttt------tagtatatttttttgaag---caacactttatgtttctataga----------------------------------------------
|||||  | || ||||||||||||||||||||||| ||||| |||||||| ||||| |||||| |    |||  |||   |  |  |       ||||| | ||    |  |  || ||||       | ||| |  || |  ||   ||| | ||| |  |  | || |                                              
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttccgttaattttagatgaacttgtaaaattattgtgatataggttggtttgttgttcaatatgtcattattgagacccaataatttgtcatgttttatatatattttttgacttattttttaaatccctctttctattcattcag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 2
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtt---tctacat---ctttgtacttaaaagtg------tttgtttggatattagttttagtatatttttttgaagcaacactttatgtt--tctataga--------------------------------------------
|||||  | || ||||||||||||||||||||||| ||||| |||||||| ||||| | |||| |    |||  |||   | || ||   ||| | |  | |  |||       ||| || | | ||   | |   ||||| ||  ||  |||||  || |  |  | |||| |                                            
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATGgtaaggccttttctgttaattgtagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattgagacccaacaacttgtcatgttttataaatatttctgaacttcttttttaaatccttgtttctatttattcag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G06960.2 (Arabidopsis thaliana), 5'ss of exon 4
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtttctacatctttg-tacttaaaagtgttt-----gtttggatatt----agttttagtatatttttttgaagcaacactttatgtttctataga
||  | ||| | || |||||||| ||||||||||||||||| ||| || | |||||||| |||||  ||  ||  | |  | |  ||   | |||  | || |||     |  | | ||||    |  | ||  || ||| || |   |  ||||||  |          
ACGCTTCGTAGGCTCGCTCAAAACCGTGAGGCTGCAAGGAAAAGCAGATTGAGGAAGAAAgtatgcttagatttatgttcatagtttcaattcttttatgttttttacaagcatagctatttgcaaactctaagatgtttgttggttactgcacttttag----------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 5'ss of exon 5
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtt---tctacatctttgtacttaaaagtgtttgtttggat------attagttttagtatatttttttgaagcaacactttatgtttctataga------------
||  | ||| | ||||||||||| |||||||| |||||||| ||| || | ||||||||||||| |    ||   ||   | ||  | ||| |||||     | | | |||  ||      ||   |   || |||  | ||||   | ||  |   |  || ||                
ACTCTTCGTAGGCTTGCTCAAAACCGTGAGGCAGCAAGGAAAAGCAGATTGAGGAAGAAGgtatattaccttccattggttttatctttttttactttttcttttctttttaaattggtgcatcgctagaagcatagctatttggtactacgttaattccttttaattgctccctccatag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 5'ss of exon 5
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtttctacatctttgtacttaaaagtgtttgtttggatattagttttagtatatttttttga-agcaacactttat-gtttctataga----------------------
||  | ||| | |||||||||||||||||||| ||||| || ||| || | ||||||||||||||| ||||||  |||     |  || |  ||     | | | ||    |  |    ||   |||| | |   | |  | |  | | |  || |  ||                        
ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAGgtatgtatattttgcttttgttcttgttttgatttttcttatatattcctcttatttccttgtaatatctctagaagaatatctatctgtcattaccttaagcatgttattgtttcctccatag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 6
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtttctacatctttgtacttaaaagtgtttgtttggatattagttttagtatattt--ttttgaagcaacactttatgtttctataga-----------------------------------------------------------------------------------------------
||||| || || ||||||||||||||||| ||||| || || |||||| ||||||| |||||| ||    ||  |     |  ||    |   |  |    |   |||   | |||  ||    | | |   |||  |||       |  ||| | | | |                                                                                                
ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgttgcacaaactgagtttctaagtgttggatagtgtattttttggttatggtttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttag

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|50331700|gb|CO526826.1|CO526826
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|89249315|gb|DY621101.1|DY621101
EST:     GCCTTGCTCACAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAA                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAAACTTTACCCCAA-TA
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAA-CTT-ACCC-AACTA
EST: gi|211521271|gb|FL055174.1|FL055174
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|211524264|gb|FL055179.1|FL055179
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAG
EST: gi|71305566|gb|DR788926.1|DR788926
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|74232819|gb|DT640733.1|DT640733
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|91872807|gb|EB402764.1|EB402764
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|60396273|gb|DN229142.1|DN229142
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|211521265|gb|FL055168.1|FL055168
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTT
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTT
EST: gi|211521270|gb|FL055173.1|FL055173
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|94472378|gb|EB701336.1|EB701336
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|211521262|gb|FL055165.1|FL055165
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATTTTCAACAGTTGGAGAATAGCA
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCA
EST: gi|71426016|gb|DR807066.1|DR807066
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|76290001|gb|DV029569.1|DV029569
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
EST: gi|211524261|gb|FL055176.1|FL055176
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATA
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATA
EST: gi|211521272|gb|FL055175.1|FL055175
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAAC
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAAC
EST: gi|211524262|gb|FL055177.1|FL055177
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAA
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGA-
EST: gi|101385511|gb|EB814802.1|EB814802
EST:     GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAG                         GCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG
genomic: GCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtat ... tattttacagGCATATGTTCAACAGTTGGAGAATAGCAGGCTAAAACTTACCCAACTAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTGCGTCGCCTTGCTCAAAATCGTGAGGCTGCAAGGAAGAGCCGACTAAGGAAGAAGgtatgtgtattttagtttctacatctttgtacttaaaagtgtttgtttggatattagttttagtatatttttttgaagcaacactttatgtttctataga

- - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG