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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGAAAGGGCAAAAAGGCAGGAAGAGGCACCACTGATTGAGCAAGCTTTTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttctactattcttttgttgtttctgcagttcagataactgtcagtgctttattaatttatttatgcttgcag

Basic information

species Zea mays
transcript GRMZM2G093050_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093050_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g03070.1 (Oryza sativa), 5'ss of exon 11
TCTGGAAAGGGCAAAAAGGCAGGAAGAGGCACCACTGATTGAGCAAGCTTTTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttctactattcttttgttgtttc--tgcagtt-cagataactgtcagtgcttt-----atta--atttatttatgcttgcag
  |||| |||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||| | |||||| |||||||| |||||||||||||| ||  ||||   || |||| ||  ||||  |  | || |  || || | |      |||       || |  ||| || | | |||| ||
CTTGGAGAGGGCAAAAAGGCAGGAAGAGGCACCTCTAATTGAGCAAGCTTTTCAAAAACGCCTTGAAGTAGAGAAAATCCTTCATGAGCAAGAGCAGCTGgtttgtttctcacaattccttgattgtcacattacaatagcatatgattacttaagctcacaaaaatcactattaatctcttcttgtag
















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|211384109|gb|FL133259.1|FL133259
EST:     CTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTT                         CGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
genomic: CTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttc ... atgcttgcagCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
EST: gi|20803164|gb|BQ294214.1|BQ294214
EST:     TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTT                         CGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
genomic: TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttc ... atgcttgcagCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
EST: gi|21891484|gb|BQ744697.1|BQ744697
EST:     TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTT                         CGGGAGATTGAACT
genomic: TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttc ... atgcttgcagCGGGAGATTGAACT
EST: gi|20508009|gb|BQ279859.1|BQ279859
EST:     TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTT                         CGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
genomic: TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttc ... atgcttgcagCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
EST: gi|213191761|gb|FM193894.1|FM193894
EST:     TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGNAAGAGCAGCTT                         CGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
genomic: TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttc ... atgcttgcagCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
EST: gi|211384102|gb|FL133252.1|FL133252
EST:     TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTT                         CGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA
genomic: TTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttc ... atgcttgcagCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGGAAAGGGCAAAAAGGCAGGAAGAGGCACCACTGATTGAGCAAGCTTTTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGCTTgtcagttttctactattcttttgttgtttctgcagttcagataactgtcagtgctttattaatttatttatgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT