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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtcatgtaaaccacagttgttgcttcagatcacagcaaatgcaatttaaattttggatcttttttttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g44220.4
intron # 12
splice site 5'
intron type U2

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|116875182|gb|EC365690.1|EC365690
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|13420391|gb|AU174481.1|AU174481
EST:     AGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: AGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|116875001|gb|EC365509.1|EC365509
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|116875027|gb|EC365535.1|EC365535
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|66915625|gb|CX102473.1|CX102473
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|1631864|gb|C19593.1|C19593
EST:     CTT-ACCTCAACCTCGATACTTACCTCCAGCAAGATTGGAGANGTNCAAG                         ATCAA-GATGCAATAATCTCCGATGGCTGTTCCT
genomic: CTTCACCTCA-CCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCT
EST: gi|88693552|gb|CI737127.1|CI737127
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|29668852|gb|CB665127.1|CB665127
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtcatgtaaaccacagttgttgcttcagatcacagcaaatgcaatttaaattttggatcttttttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT