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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatactgccggcccacaaaggtatctacaacagctagaaatattcattggcctgatcttgtagggatgcaactctgacttcttccttctttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCTAGTCGCCGTCATGATAACAGTATTTCCACCTTGTGCATCTATGAACAGG

Basic information

species Zea mays
transcript GRMZM5G862931_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862931_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g40790.1 (Oryza sativa), 3'ss of exon 5
gcatactgcc--ggcccacaaaggtatctacaacagctagaaatattcattggcctgatcttgtagggatgcaactctgac---ttcttccttctttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCTAGTCGCCGTCATGATAACAGTATTTCCACCTTGTGCATCTATGAACAGG
   || |||    ||   | | || | ||    |    |  || ||       ||| ||     ||||||   | ||||||   || ||  ||  |||||  ||||||||||| || ||||||||||| ||||| || ||||||||||| ||||||| || ||||||||||||||||||||| |||||||| || | ||| ||||
agttattgcttttgctggcgatggcaccttgtgc--tcaacaaaatctgaacaccttattc---agggatttgattctgacatgtttttaatttattttccatagAATTCATCGCAGCTGCAAGAACTTCTGGAGTACAGTAAATCAGTACCACCTAATCTCCGTCATGATAACAGTATTTCTACCTTGTGTATTTGTGAGCAGG

upper sequence: GRMZM5G862931_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g40404.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------------------gcatactgccg--gcccacaaaggtatctacaacagctagaaatattcattggcctgatcttgtagggatgcaactctgac---ttcttccttctttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCTAGTCGCCGTCATGATAACAGTATTTCCACCTTGTGCATCTATGAACAGG-------------
                                                                                      || |||    ||   ||| || | ||    |    | ||| ||      |||| ||     ||||||   | ||| ||   || ||  ||   ||||  ||||||||||| || ||||||||||| ||||| || ||||||||||| ||||||| ||             ||||||||| ||||||||||| | ||| || |             
gtgagctattttttgggcatctgcttgctcatgctaactagcaatataggaatttgcttacttgcttttggtacatcttttgtagttattgcttttgctggcaatggcaccttgtgc--tcaaaaaaatctgaacgccttattc---agggatttgattcttacatgtttttaatttactttccatagAATTCATCGCAGCTGCAAGAACTTCTGGAGTACAGTAAATCAGTACCACCTAATC-------------CAGTATTTCTACCTTGTGCATTTGTGAGCAAGGATCCAGTTTCCC
















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|78108722|gb|DV527140.1|DV527140
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
EST: gi|78108723|gb|DV527141.1|DV527141
EST:     CCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGGTGCCAAG                         AATTCATCTCATCTGCCAGAACTGCTGGACT
genomic: CCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGG-TGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACT
EST: gi|50335359|gb|CO530485.1|CO530485
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
EST: gi|60339149|gb|DN206122.1|DN206122
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
EST: gi|60348404|gb|DN215377.1|DN215377
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
EST: gi|71446368|gb|DR827418.1|DR827418
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
EST: gi|89760831|gb|DY689083.1|DY689083
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGNCA-GAACTGCTGGACTATAGTAAATCAGTGC
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTG-CAAGAACTGCTGGACTATAGTAAATCAGTGC
EST: gi|37390076|gb|CF632264.1|CF632264
EST:     CCAGG-TGACTTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
genomic: CCAGGTTGAC-TTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT
EST: gi|71446369|gb|DR827419.1|DR827419
EST:     GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAG                         AATTCATCTCATCTGCAAAAACTGCTGGACTATAGTAAATCAGTGGCACCT
genomic: GCCAGGTTGACTTGAATGAAGTATTTAACCGGCAAGCATATGGTGCCAAGgtcagtaaac ... ttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggcctgatcttgtagggatgcaactctgacttcttccttctttttcactagAATTCATCTCATCTGCAAGAACTGCTGGACTATAGTAAATCAGTGCCACCTAGTCGCCGTCATGATAACAGTATTTCCACCTTGTGCATCTATGAACAGG
                           ctctgac  putative branch site (score: 3)
                           ctctgacttcttcctt  CT-rich tract
                                         ttcttttt  TA-rich tract