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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGGGTCCACACAGCAGCTGCACCTGTGGTCACAGATCTTAGTGAAATGTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaatatatggatgctcttcatcttttgtaaatgtcaatatacatgttatatggttattacacagtttactgattatcacatcctgcag

Basic information

species Zea mays
transcript GRMZM2G081745_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081745_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g04020.1 (Oryza sativa), 5'ss of exon 10
ATCAGGGTCCACACAGCAGCTGCACCTGTGGTCACAGATCTTAGTGAAATGTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaatatatggatgctcttcatcttttgtaaatgtcaatatacatgttatatggttattacacagtttactgattatcacatcctgcag
|||||||| || |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||| || ||  |||||| |    ||||||||||| || |||| ||| ||| ||  | || || |||||     |||| | ||  |||||
ATCAGGGTGCATACAGCAGCTGCACCTGTGGTCACAGATCTTGGTGAAATGTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGAGTAGAATCGgttagtactagatttatgctcctgccattttgtaaatgccagtatatatggtatttgagtgtt-catagttt-tgacttattatatgttgcag
















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|22545799|gb|BU098173.1|BU098173
EST:     GTATCGTCAAGCAGATACTGGGGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGGGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
EST: gi|31355711|gb|CD440068.1|CD440068
EST:     GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
EST: gi|60401047|gb|DN233854.1|DN233854
EST:     GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
EST: gi|76014690|gb|DT941860.1|DT941860
EST:     GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
EST: gi|32809504|gb|CD961738.1|CD961738
EST:     GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
EST: gi|31353549|gb|CD437906.1|CD437906
EST:     GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
EST: gi|40337113|gb|CK371183.1|CK371183
EST:     GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTG                         CGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC
genomic: GTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaata ... catcctgcagCGATTGAAAATTCACTGTCTGATAAGCTGGACAGTGTCCGGCAGCAGTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAGGGTCCACACAGCAGCTGCACCTGTGGTCACAGATCTTAGTGAAATGTATCGTCAAGCAGATACTGGTGCCATTGTGTCATTGTTGGGTAGAATTGgttagtaatatatggatgctcttcatcttttgtaaatgtcaatatacatgttatatggttattacacagtttactgattatcacatcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT