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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatatcaatcctttagtgacttgttatatatcctgcagatgaactgtccctttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag

Basic information

species Zea mays
transcript GRMZM2G006452_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 5'ss of exon 17
AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatatcaatcctttagtgacttgttat-atatcctgcagatgaactgtccc--tttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag
||||||||| |||||||||||| ||||||||| |||||||||||||||||||| || || ||||| ||||| ||||| ||||||||||||||||||||| |||||||   | |||||||||  | ||| |  | || |||  | |    |   ||| || | | |  || ||  |  |||  |  | |||||    ||||  || | |||  ||| |||||
AATGACAAGTCAAAAATCAAGACAGTGATAGAAGAGTTGGATGAGAAGAAGAAAGAGACCTTGAAAGTCACATGGCTTAAAGTAAACAAgtcagtatatgaatccttctttaacttgttattgtttccagtggctgcacttgctcagactctgtatcgcggcatta-cttttctttgtaacag--acattggtagataacctctcctttccttttgtatag

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G27210.1 (Glycine max), 5'ss of exon 18
AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatatcaatcctttagtgacttgttata-tatcctgcagatgaactgtccct-ttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag
||||||||| | ||||||||||| ||||| || ||| | ||||||||||||||||| ||| | || || || ||| ||||||| || |||| |||   | |||  |||  |   ||  | || | |  | ||    |  | | | | ||  |||    |||||    |  ||  | |  ||||  ||||   |                           
AATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAAgtgagttatttaattatttt-tattttaatgtaatttgatccactcaatttatgcttgttggata----tgaaaccatttgtaagccttcgtgtataattacttt--------------------------

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 5'ss of exon 17
AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat--caatcctttagtgacttgttatatatcctgcagatgaactgtccctttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag
||||||||  ||||||||| ||||||||| |||||| | ||||||||||| || |||||  |||| || |||||| | ||||| ||| ||| ||| | |  | |  ||  |   |   ||| | | |  |||   |   ||     | |    ||| || ||   | ||| |      | | ||| ||| |  | |   |    | |||| |||   |||
AATGACAAATCAAAAATCACGAAAGTGATCGAGGAGCTTGATGAGAAGAAAAAAGAAACCCTGAAAGTTACTTGGGTTAAAGTTAACCAgtgagtgtctttctaatctccaacaaagagtt-tgtctt-tgctcttaggctcatgatct---cattcctcaa---tgtctgaaaagataatatgatattag-cctttgttaaatccttcttttttattag

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 5'ss of exon 17
AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatatcaatcctttagtgacttgttatatatcctgcagatgaactgtccctttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag
| ||||||  |||||||||||||||| || |||||| | ||||||||||| || |||||| |||| || || ||| | ||||| ||| ||| |||       |  ||||||  |||  ||  || ||    |||  |||   | ||   |||||    |  ||  || |  || | ||                                        
ACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCAgtgagt----tgcttatttagtttctt--tacttaaccatgtgattcacttctctttacgatatt-taaagttggatccttatcgttag----------------------------------------

upper sequence: GRMZM2G006452_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 5'ss of exon 17
AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatatca-atcct------ttagtgacttgttatatatcctgc--agatgaactgtccctttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag
||||||||| ||||||||||||  ||||| || ||| ||||||| ||||||||||||||||| ||||| ||||||   ||||| ||||||| ||| |||   ||| |      |||     || || ||  |  | |  | || ||   |   |||   ||||| |      | |  ||    |   ||     |   || |  | |  |   |   ||||  |   
AATGACAAGTCAAAAATCAAGATGGTGATTGAAGAGCTGGATGAAAAGAAGAAGGAAACATTAAAGGTTACTTGGACTAAAGTTAACAAgtgagtctattgcatcatgctagattacatggttcttttaattgatactaaaattaatcatttatttggttattgatctttgattttatagaacttgatgaagcttactattcataattttgtgtctcgttttcag--

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|211188348|gb|FL216446.1|FL216446
EST:     GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTTAACAA                         GGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
genomic: GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat ... gtttctatagGGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
EST: gi|211188349|gb|FL216447.1|FL216447
EST:     GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTTAACAA                         GGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
genomic: GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat ... gtttctatagGGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
EST: gi|22473074|gb|BU037554.1|BU037554
EST:     GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTTAACAA                         GGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAATT
genomic: GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat ... gtttctatagGGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
EST: gi|60342521|gb|DN209494.1|DN209494
EST:     GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAA                         GGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
genomic: GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat ... gtttctatagGGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
EST: gi|6031321|gb|AW076178.1|AW076178
EST:     GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAA                         GGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
genomic: GATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat ... gtttctatagGGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
EST: gi|26457122|gb|CA828705.1|CA828705
EST:     TTGAAGGTCACTTGGCTCAAAGTTATCAA                         GGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT
genomic: TTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatat ... gtttctatagGGATTTCGGGTCTATATTCAGTACTCTTTTACCTGGTACAATGGCAAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAAgtcagtatatcaatcctttagtgacttgttatatatcctgcagatgaactgtccctttaaatattgctgaaatgtctcttactcataagtgtgaaattggatcctaactcctacattctgtttctatag

- - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG