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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagtcatgtaaaccacagttgttgcttcagatcacagcaaatgcaatttaaattttggatcttttttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATTGAGCATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAAC

Basic information

species Oryza sativa
transcript LOC_Os01g44220.6
intron # 12
splice site 3'
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|29680979|gb|CB677254.1|CB677254
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|116875001|gb|EC365509.1|EC365509
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|66915625|gb|CX102473.1|CX102473
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|29668852|gb|CB665127.1|CB665127
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|116875027|gb|EC365535.1|EC365535
EST:     TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         ATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
genomic: TCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATT
EST: gi|7134800|gb|AU082679.1|AU082679
EST:     CTTCACCTTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAG                         NTCAAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCAT
genomic: CTTCACC-TCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATC-AAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCAT
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 420

CCTCCAAAGTTCGAATTTTATGATCCAAAAACTCCTTTCTTCACCTCACCTCGATACTTACCTCCAGCAAGATTGGAGAAGTGCAAGgtatgagtca ... ttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATTGAGCATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcttcagatcacagcaaatgcaatttaaattttggatcttttttttgtgcagATCAAAGATGCAATAATCTCCGATGGCTGTTCCTTTAGTGAATGCACCATTGAGCATTCTGTCATTGGAATCTCTTCACGCGTTAGCATCGGGTGTGAAC
                                       tcttttttttgtgc  CT-rich tract
                        aatttaaattttggat  TA-rich tract