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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttctttaaatgttttctctctgtgtcctttaatttcgtctatgcttttccatcgttcag

Basic information

species Zea mays
transcript GRMZM2G068255_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 4
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtc-tatttccttctttaa----atgt-tttctctctgtgt-cctttaatttcgtctatgcttttccatcgttcag
| ||||||||||||||||||||||||||||||||||| || || ||||| |||||||| |||||||| ||||| |||||||| |||||   |||| | |||| |||||| |     ||| |  ||| ||  ||    |||  || ||   | | |||   || |||||
GGAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAAAGCAATTGGAAAGAGAGGACCGATGTTGATGCTCTAGAAAGACAGAAGgtttgtgtcatttttctttctttgatccagtgtatcgctcccttcgtatgcttacctttgttagtacattt--gtctttcag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g45240.2 (Oryza sativa), 5'ss of exon 3
--------------GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtc-tatttccttctttaa----atgt-tttctctctgtgt-cctttaatttcgtctatgcttttccatcgttcag
              | ||||||||||||||||||||||||||||||||||| || || ||||| |||||||| |||||||| ||||| |||||||| |||||   |||| | |||| |||||| |     ||| |  ||| ||  ||    |||  || ||   | | |||   || |||||
TGACACTATTGCAGGGAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAAAGCAATTGGAAAGAGAGGACCGATGTTGATGCTCTAGAAAGACAGAAGgtttgtgtcatttttctttctttgatccagtgtatcgctcccttcgtatgcttacctttgttagtacattt--gtctttcag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttctttaaatgttttctctctgtgtcc--tttaatttcgtctatgcttttccatcgttcag-------
||||||||||||| || || || || ||| | || |||||||| ||||||||||||||||||  ||| || ||||||| ||| |||||        |  |   | | |||||| |||     ||| |    | ||  |    ||    | ||| || ||| |        
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgt-----cgcaactttctttgtaaatgatttgaaattgtttttaatgtatgtctaacttaattcttctattgtttaaatgacag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 5
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttc----tttaaatgttttctctc---tgtgtcctttaatttcgtctat---gcttttccatcgttcag-------
| ||||||||||| ||||| ||||| ||| | || |||||||| |||| |||||||||||||  ||| || ||||| | ||| ||||||    | |  ||  |      ||| ||  | | || |    |||  |||||  | |   | |      | ||| || ||| |        
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtagcaattttctttgtcaatgatttgaaattatgctgttaaatgtaaccttttgtatgaccaacttaattcttctattgtttacatggcag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttctttaa-------atgttttctctctgtgt-cctttaatttcgtcta--tgcttt-tccatcgttcag------------
| ||||||||||| ||  | || || ||| | || ||||| || ||||||||||||||||||  ||| ||  |||||||||||||||||  |    | ||   | ||||        ||||||   || ||  | |||||   |  || ||  | |||| ||||||                  
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgtttatgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag

upper sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 5
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtac-ttgtctatttccttctttaaatgttttctctctgtgtcct--ttaatttcgtctatgctt--ttccatcgttcag---------------
|||| |||||||| ||  | || || ||| | |||||||| || |||| ||||||||||||| |||| ||  |||||||||||||||||| ||   | |||  |  | ||    ||   | | | ||   |   | | || |  |||||||  ||     ||                   
GAAAATATGTTGGAAATAGGCCAATCAAACTACGTAAGAGCAATTGGAGGGAGAGGACAGATTTTGAAGCCTTGGAAAGACAAAAGgtacattaattctttggtgttgtatggcttccatgtttatgctttgccttactttgggtatgcttactttgggtgtctcctgactcacttggcag

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|211002219|gb|FL464441.1|FL464441
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGATTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|78080540|gb|DV508952.1|DV508952
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|18179346|gb|BM380556.1|BM380556
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|31612073|gb|CD568695.1|CD568695
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|32859728|gb|CD999409.1|CD999409
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|71320385|gb|DR796941.1|DR796941
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|31612074|gb|CD568696.1|CD568696
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|13150735|gb|BG321057.1|BG321057
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|74244025|gb|DT651939.1|DT651939
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|60353545|gb|DN220518.1|DN220518
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|78083193|gb|DV511586.1|DV511586
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTTTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|111145618|gb|EE257935.1|EE257935
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|60397448|gb|DN230264.1|DN230264
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|74235772|gb|DT643686.1|DT643686
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|211535630|gb|FL478811.1|FL478811
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
EST: gi|89248698|gb|DY620484.1|DY620484
EST:     AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAG                         AATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG
genomic: AGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtct ... catcgttcagAATCATGTCAAGAGGAAGCCTAAAATTCCCAAGAAGACTATTCTTCACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttctttaaatgttttctctctgtgtcctttaatttcgtctatgcttttccatcgttcag

- - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG