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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaactgatgagtgcacgtgcaaaagatcatttgtgatgaaaggtcgtggttg...

Basic information

species Oryza sativa
transcript LOC_Os04g41100.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G179097_T01 (Zea mays), 5'ss of exon 9
TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
                                 ||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | |     
---------------------------------AAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGgtaa-tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-cat-----

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G179097_T02 (Zea mays), 5'ss of exon 8
TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
   ||||| | ||||||||||||||||||| ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | || |  
---TCTTTGCGTTTTGTTTGCAAGAGACAAAAGAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGGTAA-Tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-catgatat

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G179097_T03 (Zea mays), 5'ss of exon 7
--TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
  |||||||| | ||||||||||||||||||| ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | |     
TTTGATCTTTGCGTTTTGTTTGCAAGAGACAAAAGAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGgtaa-tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-cat-----

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 8
--TGATCTTTCCATTTTGTTTGCAAGAGACAAGAGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgacta-aaactgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
  |||||||| ||||||||||||||||||| | ||||||| |||||||||| ||||||||||||| | ||||||||||||| ||| |||||||||||  ||||||| ||||| ||||| ||| || |  ||||||| || ||||| |||| ||||| ||||  |   | |          ||| ||||  ||     || ||         
TTTGATCTTTGCATTTTGTTTGCAAGAGACGAAAGAAGCGCAGGGGAAGGAAGCCTTTTGCTTTT-ATCAGGAAATCAATG-ACATTAATACAACTTAGAAGgtaa-tatat-caaaagccaattgctgcaagtgacgtgttgctaactagaaactaatgaacgagggagttctttactgaaaaatcaggtgcatgaaatggat-------

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|88291287|gb|CI529877.1|CI529877
EST:     TTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTNTGGCTGGTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: TTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|29626550|gb|CB631561.1|CB631561
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|87021463|gb|CI274070.1|CI274070
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|27920887|gb|CB096695.1|CB096695
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|218495458|gb|FG950145.1|FG950145
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
EST: gi|88286911|gb|CI520221.1|CI520221
EST:     GGACAGTAATACAACTTGAAAG                         CTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT
genomic: GGACAGTAATACAACTTGAAAGgtaaatatat ... acgtctgcagCTTAAGCTGTGGCTGCTTCAAGATAGGAAGCTTGATGGCCCTCAGCTTGTT