Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgcctctctatttcagtttttcttttggatagtattatgttatttccttattttctaatcgatttgtatctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCTCAAATAGCATTCCCATAAGAGGAAGAAGGCCATACTGAGGGCGGCAAAA

Basic information

species Oryza sativa
transcript LOC_Os01g68320.1
intron # 9
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|29643632|gb|CB648639.1|CB648639
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|29678104|gb|CB674379.1|CB674379
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88429964|gb|CI562775.1|CI562775
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|86860514|gb|CI323438.1|CI323438
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGTTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|89178234|gb|CI391413.1|CI391413
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTCCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|29661778|gb|CB658053.1|CB658053
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88480999|gb|CI418270.1|CI418270
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|58685731|gb|CK074418.1|CK074418
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|29633339|gb|CB638348.1|CB638348
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88486606|gb|CI423877.1|CI423877
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCNTGGTGGGTTTGGTAACAAATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88514918|gb|CI442572.1|CI442572
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGNTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|55411539|gb|CV723915.1|CV723915
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88505927|gb|CI433433.1|CI433433
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|29643631|gb|CB648638.1|CB648638
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTATATGGGAG                         GAGGCAATTTCGGGTNAAGGGG
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGG
EST: gi|88548417|gb|CI476788.1|CI476788
EST:     T-TGAATCCAGCGCTAGAATCTATGGCTAAATGTNCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCNTGGTGGGTTTAGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|218490541|gb|FG963338.1|FG963338
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88470527|gb|CI407798.1|CI407798
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGNTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|15008370|gb|AU222758.1|AU222758
EST:     AATCCAGCCGCTANAAATCTATGGCTAAATNTGCCAGTTCTTATGGGAG                         NAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGC
genomic: AATCCAG-CGCTA-GAATCTATGGCTAAATCTGCCAGTTC-TATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGC
EST: gi|88446842|gb|CI528885.1|CI528885
EST:     ATCCAGCGCTAGAATCTATGGCTAAATCTNCCAGTTTTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: ATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|86869051|gb|CI335618.1|CI335618
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88266160|gb|CI377062.1|CI377062
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88980895|gb|CI021022.1|CI021022
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|29662446|gb|CB658721.1|CB658721
EST:     TGTGAATCCAGCGCTAGAATTTATGGGTAAATCTGCCAGTTTTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88261652|gb|CI365228.1|CI365228
EST:     TTTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCC-GTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88982709|gb|CI028122.1|CI028122
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|86878096|gb|CI328626.1|CI328626
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88257882|gb|CI360468.1|CI360468
EST:     TTTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGTTAACAGACCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|29669297|gb|CB665572.1|CB665572
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
EST: gi|88440085|gb|CI546380.1|CI546380
EST:     TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAG                         GAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT
genomic: TGTGAATCCAGCGCTAGAATCTATGGCTAAATCTGCCAGTTCTATGGGAGgtaggtgcct ... ctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatagtattatgttatttccttattttctaatcgatttgtatctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCTCAAATAGCATTCCCATAAGAGGAAGAAGGCCATACTGAGGGCGGCAAAA
                            ttctaat  putative branch site (score: 2)
        tattatgttatttcct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgcctctctatttcagtttttcttttggatagtattatgttatttccttattttctaatcgatttgtatctgtgtttagGAGGCAATTTCCGGTCAAGGGGGCGTGGTGGGTTTGGTAACAGATCTGGCTCAAATAGCATTCCCATAAGAGGAAGAAGGCCATACTGAGGGCGGCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG