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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcactatgtattacactattgcataatgagtttacctttaccttttgtctttgtatctctttattaacaagggggcatattcattgtcactttt...

Basic information

species Zea mays
transcript GRMZM2G002859_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcactatgtattacactat-tgcataatgagtttacctttaccttttgtctttgtatctctttattaacaagggggcatattcattgtcactttt
 ||||||||  ||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||||| |  | ||| | |  |  |    |      || ||| ||||  | ||   |  |  | ||||    | | |   | || | |  |  
GGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCACAGgttatctcactatgaaacatactgtctttactacccttcatatgttgcctattgttatggtgatttctattaaacatactgtctttaccctttttatctg-

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G01120.2 (Glycine max), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttca---ctatgtattacactattgca-taatgagtttacct-ttacct-tttgtctttgtatctctttattaacaagggggcatattcattgtcactttt---------------------------------------------------------------------
|||||| ||  | || || ||||| ||||||||||| ||||||||||| || || ||||||||| | || ||||||||||| || ||||| ||||| |||||   |  |    ||| | | |   ||||| | |  |   ||||  | | |||   ||   |||  |    | | | ||  ||     || |||||      ||||                                                                     
TGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCCAGgtatctggaattttatctttcattttattgtacttttttttttatttgtcaccagcttacattttgagaaatgtctgaatgagtaactat-ttcatcaatgatttttttcctttgtactttgtaattacactgtcttttaaacctagacaggctattgaagtttccaaacgccag

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G11950.3 (Glycine max), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcactatgtat------tacactattgcataatgagttta----cctttaccttttgtc--------tttgta-tctctttatta-acaagggggcatatt-cattgtcactttt------------------------------------------------
|||||| ||  | ||||| |||||  |||||||||| |||||||||||| | || ||||||||| | || ||||||||||| || ||||| ||||| ||||| |||  | ||| |||      |  |   || || ||   |||      |||||  | ||||||        |||||| ||| | |  |        | |||| || ||||     ||||                                                
TGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTAGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCGGAAGCCCAGgt-attcgagtatttatctttcatttaacttttcaaaacttgttggacatcctttttcatttgtcacctgctttttgtagtctgtcttctgtgtttcagtgcatgtttcattaatgattttattttactattttgtggtgtaattactctgtcttttgaacctagacag

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G01100.2 (Glycine max), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcactatgtattacactattg-cataatgagtttacctttaccttt-----tgtctt--tgtatctctttattaacaagggggcatattcattgt-cactttt-----------------------------
|||||| ||  |||| || ||||| ||||||||||| ||||||||||| || || ||||||||| | || ||||||||||| || ||||| ||||| ||||| || |     | ||||  ||| ||  |||        | | |  |  ||      |||||   ||  | ||| | | | ||| |     | ||   | |  ||||||                             
TGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCACAGgt-atctggaattttattgtacttttttcatttgtcacctgcttacattttgggaaatgtctgaatgagtatctgtttcatcaacgatttttttttcctatgtactttttaattacactgtcttttaaacctagacag

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G04210.1 (Glycine max), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttc-actatgtattacacta----ttgcataatgagttta----cctttaccttttgtc------tttgtatctctttatta-acaagggggcatatt-cattgtcactttt------------------------------------------------
|||||| ||  | ||||| |||||  |||||||||| |||||||||||||| || ||||||||| | || ||||||||||| || ||||||||||| |||||| | |  | | | | || || |     || || ||   |||      |||||  | ||||||      ||| | ||| | |  |        | |||| || ||||     ||||                                                
TGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCCAGgtgttctagaatttatctttcatttaacttttcaaaacttgttggacatcctttttcatttgtcacctgctttttgtctgtcttctgtgtttcagtgcatgtttcattaatgattttattttattattttgttgtgtaattactctgtcttttgaacctagatag

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G01120.1 (Glycine max), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttca---ctatgtattacactattgca-taatgagtttacct-ttacct-tttgtctttgtatctctttattaacaagggggcatattcattgtcactttt---------------------------------------------
|||||| ||  | || || ||||| ||||||||||| ||||||||||| || || ||||||||| | || ||||||||||| || ||||| ||||| |||||   |  |    ||| | | |   ||||| | |  |   ||||  | | |||   ||   |||  |    | | | ||  ||     || |||||      ||||                                             
TGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCCAGgtatctggaattttatctttcattttattgtacttttttttttatttgtcaccagcttacattttgagaaatgtctgaatgagtaactat-ttcatcaatgatttttttcctttgtactttgtaattacactgtcttttaaacctagacag

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgt---------gatttcactatg----tattacactattgcataatgagttta--cctttaccttttgt-----ctttgtatctctttattaacaagggggcatattcattgt-cactttt--------------
||| || ||  |  |||| |||||| |||||||||| |||||||||||| | || ||||||||| | || ||||||||||| |||||||||||||| |||||         |||   || |||    ||||  | ||  |      || | |     ||| ||| ||       ||    || |  |||||  || |   | |  ||  || | | | |                
TGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTCAGgtacggtgaaagataataccatgaagctatttaattaccgttagtagaatatgggttttttcctcttccaagaactagtcattttattattcgcatgatagaactttacttatgcgcctgctttaatccaaacag

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttca--ctatgtattacactattgcataatgagtttacctttaccttttgtctttgtatctctttattaacaagggggcatattcattgtcactttt
|||||| ||  | || || ||||| ||||||||||| |||||||||||||| || ||||||||| | || || |||||||| |||||||||||||| |||||  | | |  | || |  |  | | || || ||||  |  || |||  | |  |  ||      | |||  ||           |  | | | |   ||| 
TGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTCAGgtattcttaaacaattttatttagtttttca-aatgtatgcacttttctcctagggtttgagtcatatttgatattttcttttattgctgagtttttgttt-

upper sequence: GRMZM2G002859_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 5'ss of exon 5
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac-tatgtattacactattgcataatgagtttacctttaccttttgtctttgtatctctttattaacaagggggcatattcattgtcactttt-
|| ||||||  | || || ||||| ||||||||||| |||||||||||||| || ||||||||| | || || ||||||||    ||||||||||| ||||| |  | |  ||||    |     ||  ||    ||| | |      | | |  | ||   |  |   |||    || |      ||||||||||  ||  
TGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTCAGgtaacgttagatatgagacatttctttatatctgcagtctgctggatgcatcttccatttcttaccaaaatt--tgagcgattcatttcattgtcatattcc

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|148932010|gb|EC875305.2|EC875305
EST:     GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCGAAGCGCCNAATGAAACTA
genomic: GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac ... agttctgcagGCTATTGAAGTTTCGAAGCGCCAAATGAAACTA
EST: gi|50324117|gb|CO519243.1|CO519243
EST:     GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
genomic: GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac ... agttctgcagGCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
EST: gi|71307048|gb|DR789679.1|DR789679
EST:     GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
genomic: GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac ... agttctgcagGCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
EST: gi|148959420|gb|EC905446.2|EC905446
EST:     GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
genomic: GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac ... agttctgcagGCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
EST: gi|148986437|gb|EE030179.2|EE030179
EST:     GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
genomic: GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac ... agttctgcagGCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
EST: gi|21987351|gb|BQ778879.1|BQ778879
EST:     GCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAG                         GCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT
genomic: GCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcac ... agttctgcagGCTATTGAAGTTTCGAAGCGCCAAATGAAACTAAGAGAGGCGTCTGGAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGCAGgtgatttcactatgtattacactattgcataatgagtttacctttaccttttgtctttgtatctctttattaacaagggggcatattcattgtcactttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC