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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaactgtatttcaactttttattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG

Basic information

species Oryza sativa
transcript LOC_Os04g46570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G101181_T03 (Zea mays), 3'ss of exon 3
gtacaactgtatttcaactttttattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
|||  | ||  || |||  | |  |||  ||| ||| ||| |||| |||| ||||| ||| ||| ||||| || |||||||||||||||||||| || ||| | || |||||||||||||||||||||||||||||||| |||||||| |||||||| || || ||
gtatgattgccttccaatgtctggttgatttgtttt-tatcatcccttgtgttacctttatgatgttcagcttgcagATAACAGATGCTGTTGTAGTTGCCTGGATTTTGAATGCCACACTTGTTGTACCTGAGTTAGACCACCACTCGTTCTGGAAAGACGACAG

upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
-------------------gta--caactgtatttcaacttttt-attgcgttgctttgtattatccattgtattaccattacgatcttcagttt--ccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
                   |||  | | || || | |  ||| | | |   ||  |    |   | | |  | |    || || ||| |    ||  ||||||||||||||| |||||||| ||  ||||  | ||||| ||||| |||||||||||||| ||||| || || || ||||| ||||| ||
ggaggctcagattctttctgtagtctaatgaatataatttttctcaattaattaataaacaa-gttcttcctgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG

upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 4
-------------------------gtacaactgtatttcaactttttattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
                          |  |  | | ||| ||  |   | ||      ||  |  |||  |    |    ||| | | || |  |  ||||||||||||||||||||||||| ||||||||  | ||||||||||| || ||||| ||||| ||||| || || |  ||||||||||| ||
gttagtttcctagtcaggctcataattttatatatttttaaaaataaaaatgaacaagttctttctatggaaatgacactcatcatgttcct--gcatccagATAACAGATGCTGTTGTTGTTGCCCGAATTCTTAATGCCACACTAGTAGTACCGGAGTTGGATCATCATTCTTATTGGAAGGATGACAG

upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G41740.1 (Glycine max), 3'ss of exon 3
-------------------------gtacaactgtatttcaactttttattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
                          |  |  | | ||| ||  |  || ||  |   ||  |  | |  |    |  | ||| | | || |  |   |||||||||||||||||||||||| || |||||  | ||||||||||| || ||||||||||| ||||| || || |  ||||| ||||| ||
gttctctttcctagtcaggcagatgatttatttatttttaaaaataataatgaataatttcttcctgtggaaatgacaatcatcatgttcct--gcacccagATAACAGATGCTGTTGTTGTTGCACGAATTCTTAATGCCACACTAGTAGTACCTGAGTTGGATCATCATTCTTATTGGAAAGATGACAG

upper sequence: LOC_Os04g46570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G15170.1 (Glycine max), 3'ss of exon 3
---------------gtaca-actgtatttcaactttttattgcgttgctttgt--atta-tccattgtattaccattacgatc----ttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
                | || |   | ||||   |||||  |   ||  ||  |  |  | | | |  | |    || || |||    |   || |||||||||||||||| |||||||| ||  ||||  | ||||| ||| | |||||||||||||| ||||| || || || ||||| ||||| ||
tctctctgtagtctaatgcatataatttttctctttttttctcaattaattaattaaccagttcttcctgtggaaatgacaatcatattcttgtctccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACATTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG

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|4715473|gb|AU056590.1|AU056590
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         ATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTA
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTA
EST: gi|33675275|gb|CF303514.1|CF303514
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         T
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccag-
EST: gi|33675275|gb|CF303514.1|CF303514
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         T
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccag-
EST: gi|33675275|gb|CF303514.1|CF303514
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         T
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccag-
EST: gi|33675275|gb|CF303514.1|CF303514
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         T
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccag-
EST: gi|33675275|gb|CF303514.1|CF303514
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         T
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccag-
EST: gi|33675275|gb|CF303514.1|CF303514
EST:     GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGG                         T
genomic: GTTACTTGCTGATTGGTACTAGCGGGGGACTAAATCAGCAGCGCATAGGGgtacaactgt ... cagtttccag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG
                                         tcttc  CT-rich tract
           tttgtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaactgtatttcaactttttattgcgttgctttgtattatccattgtattaccattacgatcttcagtttccagATAACAGATGCTGTTGTTGTCGCCCGAATATTGAATGCCACACTTGTTGTACCTGAGTTAGATCACCACTCATTCTGGAAGGATGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG