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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctacctcagacccactcatgtgggagcctccggcactgggtctgccctttaaaaagaatcaatgtgaatggtactttctaatacttttctgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTCTGTTCTGTACTTGGCATGGATTTTGTGGGCACTGTTACTAAAGTTCATC

Basic information

species Zea mays
transcript GRMZM2G112337_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112337_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 4
cctacctcagacccactcatgtgggagcctccggcactgggtctgccctttaaaaagaatcaatgtgaa-tggtactttctaatacttttctgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTCTGTTCTGTACTTGGCATGGATTTTGTGGGCACTGTTACTAAAGTTCATC
   |  |         | || |  |         |||    ||  |  |||||||   ||  |  |||| | ||| ||  |   | |||  |||||||||||| | ||| ||    | ||||||||| | ||||||||||||||| |||||||||||||| ||||| ||||||||  || ||||||||||| |||||||||
-tgatatagctgatgataatctttgcattatacacacattttcgactatttaaaatttattgacttgaaatcgtatttctttccattttcttgcattgcagAGCAATAGACTGCACAAGATTCTTGACTTCGTGAGTTCAGTGCATGATCTCTGTTCTGTCCTTGGGATGGATTTCCTGAGCACTGTTACTGAAGTTCATC
















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|76289491|gb|DV029059.1|DV029059
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
EST: gi|148930867|gb|EC873288.2|EC873288
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTTGAGT-CAGTGCACGATCT
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGT-GAGTTCAGTGCACGATCT
EST: gi|148999825|gb|EE036849.2|EE036849
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAAGT-CAGTGCACGATCT
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGA-GTTCAGTGCACGATCT
EST: gi|149096273|gb|EE181983.2|EE181983
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
EST: gi|148964767|gb|EC906024.2|EC906024
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
EST: gi|148995698|gb|EE034921.2|EE034921
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGA
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGA
EST: gi|149015047|gb|EE044793.2|EE044793
EST:     GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
EST: gi|71324224|gb|DR798815.1|DR798815
EST:     GGAGATTAAATGAATATCTTTCCGAACTACTAGCCCTGCAAAAGGAAAAG                         AGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC
genomic: GGAGATTAAATGAATATCTTTCTGAACTACAAGCCCTGCAAAAGGAAAAGgttgtttact ... tgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttaaaaagaatcaatgtgaatggtactttctaatacttttctgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTCTGTTCTGTACTTGGCATGGATTTTGTGGGCACTGTTACTAAAGTTCATC
                               ttctaat  putative branch site (score: 2)
                                     tacttttct  CT-rich tract
     taaaaagaatcaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctacctcagacccactcatgtgggagcctccggcactgggtctgccctttaaaaagaatcaatgtgaatggtactttctaatacttttctgcattgcagAGTACTAGGCTCTCAAGGATTCTTGAATCCGTGAGTTCAGTGCACGATCTCTGTTCTGTACTTGGCATGGATTTTGTGGGCACTGTTACTAAAGTTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA