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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattgtgttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g04190.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 3
------------------------------------------------gtatgtattgtg--ttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG-----
                                                | ||| |   |   || |||  |   | ||| || || || ||| ||   |||  |  |   |||  || | | |   ||| | ||   ||| || | | ||| | ||| ||  |   |||| |     |     || ||   || || |||||||| ||||| ||||||||||| || ||||| ||||| ||| |||| |||||||| || || |     
gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaata-atgagctggaagtata-aca-gttacatcttttctgcacttctgttg-tggaca-caaaaactgttagtt---aatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------gtatgtattgtgttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacaca-ttccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG
                                               |   ||  |  |   |   | || |||     |     ||  ||     |     |   | | | |||| | |   ||| | |||  ||| |||| | ||| | ||| || ||   |||| |     |  | ||  ||   || || |||||||| || || |||||||||||||| ||||| ||||||||| |||| ||||| || ||||| |
gtatgtactttatcactactacaagatgattgtttcttaaacacaattggataaagcataatttactgcattttaattgatgaaaatgaataacaagctgaaaataaaatagttccatcttttctgcacttatcttg-tgaaca-caaaaactgttagat---aataccaggaatccatttcatggaatgtagTGTGGTCAATGGTGCGCTTGAATATCTTGCGAAGGATCTTGGAATTGCTGAAAATGCCGTCTTACAGG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 3
----------------------------------------------gtatgtattgtgttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacaca-ttccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG
                                               |   ||  |  |   |   | || |||     |     ||  ||     |     |   | | | |||| | |   ||| | |||  ||| |||| | ||| | ||| || ||   |||| |     |  | ||  ||   || || |||||||| || || |||||||||||||| ||||| ||||||||| |||| ||||| || |||||  
gtatgtactttatcactactacaagatgattgtttcttaaacacaattggataaagcataatttactgcattttaattgatgaaaatgaataacaagctgaaaataaaatagttccatcttttctgcacttatcttg-tgaaca-caaaaactgttagat---aataccaggaatccatttcatggaatgtagTGTGGTCAATGGTGCGCTTGAATATCTTGCGAAGGATCTTGGAATTGCTGAAAATGCCGTCTTACAG-

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 7
------------------------------------------------gtatgtattgtg--ttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG
                                                | ||| |   |   || |||  |   | ||| || || || ||| ||   |||  |  |   |||  || | | |   ||| | ||   ||| || | | ||| | ||| ||  |   |||| |     |     || ||   || || |||||||| ||||| ||||||||||| || ||||| ||||| ||| |||| |||||||| || || |
gtatgtactttattgctgctacaagatgcttgtttcttaagcacaattggatgaagcataatttactgcattttaattgacaaaaatgaata-atgagctggaagtata-aca-gttacatcttttctgcacttctgttg-tggaca-caaaaactgttagtt---aatagcatgaatccgtgttatggaatgtagTGTGGTCAATGGCGCACTTGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG

upper sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtattgtgttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG
                               |  |  |   ||  ||| |||   || |      |    | |||| |        ||  |||  |||  ||     ||||  | |  |||   |||||  |||||    |  ||| ||||| || || ||||||||||| ||| | ||||| ||||||||| |||| |||||||| |||||||
-------------------------------aatacagttaagtctttttgtatgcaacagggtctcatgtataactt--------atctatgggtaa-gatgtactgtaa--cagtgtatgctattttttatttg----ccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG

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|88738909|gb|CI762417.1|CI762417
EST:     TATATGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGG                         AGTGGTCAACAGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA
genomic: TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGGgtatgtattg ... tgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA
EST: gi|88385512|gb|CI564172.1|CI564172
EST:     TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGG                         AGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA
genomic: TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGGgtatgtattg ... tgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA
EST: gi|88368202|gb|CI575084.1|CI575084
EST:     TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGG                         AGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA
genomic: TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGGgtatgtattg ... tgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA
EST: gi|300215629|gb|HO088255.1|HO088255
EST:     TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGG                         AGTGGTCAATGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTGCTGA
genomic: TATGTGGGCGTTGCTTGTTTGGGGGCTATTTTATTTGGTTATCATCTTGGgtatgtattg ... tgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG
 gaataac  putative branch site (score: 2)
                                 attttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattgtgttgctgtttccaatttgtcataattgcatagattttctgtcaccacccacacattccttgtaacctgaatttaaattgatgaataacaatacctggtaaatctgaatatctcattttgaatttgtgttctgcagAGTGGTCAACGGCGCTCTTGAATATCTTGCAAAGGACCTTGGAATTTCTGAGAATGCTGTGTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG