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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatatcttgtgatggctatttcatattgttttacatgcaaatataattttgattatttcagatcacattcacattccatataatgtgttggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACTAGGCGTGGTCAAGTGCTTGAAGTCGATGGGGAGAAAGCTGTTGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g51380.1
intron # 3
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|88352648|gb|CI624587.1|CI624587
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88724403|gb|CI747662.1|CI747662
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88433134|gb|CI569803.1|CI569803
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|58672899|gb|CK061585.1|CK061585
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88358211|gb|CI605136.1|CI605136
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88360936|gb|CI625242.1|CI625242
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|163927702|gb|EG710506.1|EG710506
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88317359|gb|CI628008.1|CI628008
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88345261|gb|CI627902.1|CI627902
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88397163|gb|CI593375.1|CI593375
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88371072|gb|CI597549.1|CI597549
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88360978|gb|CI625284.1|CI625284
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|86901596|gb|CI310358.1|CI310358
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGGGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88356589|gb|CI626204.1|CI626204
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88724311|gb|CI747570.1|CI747570
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88314360|gb|CI604844.1|CI604844
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|88388263|gb|CI627802.1|CI627802
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
EST: gi|66915737|gb|CX102585.1|CX102585
EST:     GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAG                         GGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT
genomic: GGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAGTGAAGgtaatcatat ... ggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttgattatttcagatcacattcacattccatataatgtgttggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACTAGGCGTGGTCAAGTGCTTGAAGTCGATGGGGAGAAAGCTGTTGTTCAG
  ttttgat  putative branch site (score: 4)
     tgattattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcatatcttgtgatggctatttcatattgttttacatgcaaatataattttgattatttcagatcacattcacattccatataatgtgttggtatttcagGGTCCTAAATACCAAGAAATTGTCAATATACGATTAGGAGATGGCACAACTAGGCGTGGTCAAGTGCTTGAAGTCGATGGGGAGAAAGCTGTTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT