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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatcattagctgagtttctggatcctgattttttttcaacagtatatatgctgtgttgcctatgaagttgggttcactgtttttcatatcccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA

Basic information

species Oryza sativa
transcript LOC_Os04g57320.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G102349_T02 (Zea mays), 3'ss of exon 7
tgatcattagctgagtttctggatcctgattt----tttttcaacagtatatatgctgtgttgcctatgaagttgggttcactgtttttcatatcccgt-tgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA
      ||  |||  ||   |  ||||||  |      |||  || |  | | |  |    |||| || |   ||   | | |  |       |||| | |||||||||||||||||||||||| ||||||||||||||||| |||||||| || |||||||| |||||||| ||||||||||||||||  ||||||||||||||
----tgtttactggattctggcctcctgacgtgaaccatttgtactgcctttctatttctctgcc-ataagactgttgtaagtactcactgattcccatatgcagATAACTTGTATGATGTATTCGTCAATATACGAGATGACGAGGCAGAGCACTGCAAGACAATGAAGGCATGTCAAACACATGGAACTCTTCGTTCTCCTCA

upper sequence: LOC_Os04g57320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G010555_T01 (Zea mays), 3'ss of exon 8
tgatcattagctgagtttctggatcctgattt---tttttcaacagtatatatgctgtgttgcctatgaagttgggttcactgtttttcatatcccgt-tgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA
      ||  |||  ||   |  ||||||| |   || ||            | || | |  | |  | || |    | | |        | ||   | |||||||||||| || |||||||| || ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||| ||||||||||||||
----tgtttactggattctggcctcctgatgtgagttatttgtagtcgagctttctatttctcttccgtaggtctcgtaaataaacgctgtttcatatatgcagATAACTTATACGATGTATTCGTTAATATACGAGAAGATGAGGCAGAGCACTGCAAGACAATGAAGACCTGTCAAACACATGGAAATCTTCGTTCTCCTCA

upper sequence: LOC_Os04g57320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G01130.1 (Glycine max), 3'ss of exon 8
tgatcattagctgagtttctggatc-ctgattttttttcaacagtatatatgctgtgttgcctatgaagttg--ggttcactgttt-ttcatatcccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA
   |  |   ||||        ||  |   |||   || |||  | |  |||| ||   |  | | |  |||  | || ||  | | || || |||| |   ||| ||  |||| ||||||||||| || ||  |||||||||| || |||||||| ||||| |||||||| |||||||| ||||| ||||| || || |||||
---ttgtctcctgaacaaaccaattacctctttgcattgaacctttttaatgcagtaaagtttctcacattgatgattaacaatatatttatttcccatc-tagAGAATCTGTACGATGTATTTGTAAACATCAGAGATGATGAAGCTGAACATTGTAAGACAATGAAGGCTTGTCAAACCCATGGGAACCTCCGGTCACCTCA

upper sequence: LOC_Os04g57320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G11950.1 (Glycine max), 3'ss of exon 8
tgatcattagctgagtttctggatcctgattttttttcaacagtatatatgctgtgttgcctatgaagttg--ggttcactgttt-ttcatatcccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA
  |||  |  |  |    |   || |   ||| | || |||  | || |||| ||   |  | | |  |||  | || ||    | || || |||| |   ||| ||  |||| ||||||||||| |||||  ||||||| || || |||||||| ||||| |||||||| |||||||| ||||| ||||| || || |||||
-aatctctcccgaacaaaccaaatacctctttgtattgaacctttta-atgcagtaaagtttctcacattgatgattaacaacatatttatttcccatc-tagAGAATCTGTACGATGTATTTGTAAATATCAGAGATGACGAAGCTGAACATTGTAAGACAATGAAGGCTTGTCAAACCCATGGGAACCTCCGGTCACCTCA

upper sequence: LOC_Os04g57320.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0523g00040.t01 (Vitis vinifera), 3'ss of exon 4
-tgatcatta--gctgagtttctggatcctgattttttttcaacagtatatatgctgtgttgcctatgaagttgggttcactgtttttcatatcccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA
 | ||  |||   |  ||| |   || | | |   |  ||   || || | || ||   ||||   |         |||||| |||||    | |  || |||| |||||||| || || ||| | |||||  |||||||||| |||||||| |||||||| ||||||||||| || || ||||| || || || ||||||||
gttattgttatcacctagtcttcagaacataacaatggtttc-cactacaaattctac-ttgctcctc--------ttcactattttttcctttc--tttcagAGAACTTGTACGACGTGTTTCTGAATATCAGAGATGATGAAGCAGAACACTGCAAGACAATGAAGGCCTGCCAGACTCATGGGAATCTCCGGTCTCCTCA

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|29673916|gb|CB670191.1|CB670191
EST:     CGATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTG                         ATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
genomic: CGATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTGgtacggatgt ... cccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
EST: gi|86860250|gb|CI323283.1|CI323283
EST:     ATGAGTTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAAGTG                         ATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
genomic: ATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTGgtacggatgt ... cccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
EST: gi|25798460|gb|CA754421.1|CA754421
EST:     TTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTG                         ATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
genomic: TTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTGgtacggatgt ... cccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
EST: gi|87007304|gb|CI278975.1|CI278975
EST:     ATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTG                         ATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
genomic: ATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTGgtacggatgt ... cccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
EST: gi|29661402|gb|CB657677.1|CB657677
EST:     ATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTG                         ATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAAAACATT
genomic: ATGAATTTCAAACAGCAAGAGTCCCATGTTCTAGGAGACCTAAAATTGgtacggatgt ... cccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT
EST: gi|29661403|gb|CB657678.1|CB657678
EST:     CAAGAGTCCCATGTTCTAGGAGACCTAAAATTG                         ATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAAAACATT
genomic: CAAGAGTCCCATGTTCTAGGAGACCTAAAATTGgtacggatgt ... cccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgctgtgttgcctatgaagttgggttcactgtttttcatatcccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA
                                            tcccgtt  CT-rich tract
                                   tttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatcattagctgagtttctggatcctgattttttttcaacagtatatatgctgtgttgcctatgaagttgggttcactgtttttcatatcccgttgcagATAACTTGTATGATGTATTTGTCAATATACGAGATGATGAGGCAGAACATTGCAAGACGATGAAGGCCTGTCAAACACATGGAAACCTTCGTTCTCCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC