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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatatttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcag

Basic information

species Zea mays
transcript GRMZM2G399073_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 5
AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgttttttc------atctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatatttgttt----aatattactgt---tctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcag
|| |||||||| || |||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||| |||||||| || ||||| ||||||||||||  |  ||       || | ||     | | |||| | ||   |  |       ||  || ||||   | |||||      ||| ||||       | || | ||||  |||   | | ||   ||||  ||| |||||||  ||||
AAGGAGAAGAAGATTCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTCATTAAGAACCTTGGGACCATTGCCAAATCTGGAACTTCAGgtattactcctttgtactgatttctcttaaagttatgtgtattctcttgctaaaactttagtattatctatttgtttgtaaagagaattttaccaagtgccatttaacttaaactt--gagtgataccaattccttgaaattttt--gcag

upper sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 5
-AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatat-ttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcag
 || || |||||||| ||||| ||||| || || |||||||||||||| ||||||||| | || || ||  | || || || || || ||||| ||||| ||||| || | ||     ||  |||  |||  || | |  | | |||| ||   |||    |  ||| || ||  ||     |  ||||  ||||                                             
CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtat-gtatgtt-----gt--ggcacattgctgaagt--agtttttgcttgtaatgtggttgggaagatgttaattggagctg-tgttaattca---------------------------------------------
















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|148965480|gb|EE016290.2|EE016290
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
EST: gi|56538364|gb|CX054073.1|CX054073
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTTAG                         CTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
EST: gi|149004856|gb|EE039364.2|EE039364
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
EST: gi|24767582|gb|CA402726.1|CA402726
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
EST: gi|31360086|gb|CD444443.1|CD444443
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTGGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
EST: gi|148964727|gb|EC905993.2|EC905993
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
EST: gi|149112828|gb|EE295636.2|EE295636
EST:     GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAG                         CTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT
genomic: GGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgtttt ... ttttttgcagCTTTTGTCGAAAAGATGCAGTCTGGAGGTGACCTCAATCTTATTGGACAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatatttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT