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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGAATACAATAGACGCCCGGAGTTCTGTAATTTTCGACAGTCGTTTCTATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaatatctatctgctggtagtgattgctgaattttctcccttttggctaacaatgttttatatgcgtttgacag

Basic information

species Oryza sativa
transcript LOC_Os07g31460.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g31460.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G474236_T01 (Zea mays), 5'ss of exon 8
CCTGGAATACAATAGACGCCCGGAGTTCTGTAATTTTCGACAGTCGTTTCTATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaatatctatctgctggtagtgattgctgaattttctccc----ttttggctaacaatgttttatatgcgtttgacag-----------------------
||||||||| | | || || |||| ||| | ||| ||||| || |||||| |||||||||||||| ||||| ||||||||||| ||||||||||| ||| ||| ||| | ||| |||| | ||| | ||| | |||| || ||| ||||| | || | |
CCTGGAATATACTTGATGCTCGGAATTCAGAAATGTTCGAGAGCCGTTTCCTGAGGAAAACATTTACAGTGGATAAGAGATATAAGGCAAATGCTTTCAGgtgggttttatacc-atcggctgatgactgatgcacactttgtccaagtagttttagcgaaccatgttccttctg-accgaattgcttgctctattttcctttggcag
















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|29616585|gb|CB621597.1|CB621597
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|157651519|gb|EX451153.1|EX451153
EST:     TAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTTG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|29624539|gb|CB629550.1|CB629550
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|29676466|gb|CB672741.1|CB672741
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTTTGCGAGTGAGAGAATTTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|27548254|gb|CA766230.2|CA766230
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|29659966|gb|CB656241.1|CB656241
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|86900017|gb|CI300115.1|CI300115
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|29621977|gb|CB626988.1|CB626988
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTTTGCGAGTGAGAGAATTTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
EST: gi|29681352|gb|CB677627.1|CB677627
EST:     TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCG                         GTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT
genomic: TATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaa ... cgtttgacagGTTTCGGTTTCTGCGAGTGAGAGAATCTAATGGCAATCCAAGGTTTCAGAT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGAATACAATAGACGCCCGGAGTTCTGTAATTTTCGACAGTCGTTTCTATAGGAAAACATTTACTGTGGACAAGAGATATAAAGCAAATGCTTTTCGgtatgttcaatatctatctgctggtagtgattgctgaattttctcccttttggctaacaatgttttatatgcgtttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA