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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcacagtaatctgcttggtagcagtaaaataatactctattgtctgaccacatttatttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 11
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgt----atggcacagtaatctgcttggtagcagtaaaat-aatactctattgtctgaccacatttatttttcag
| | ||||| |||||||||||||||||||| |||||||| ||||| || || |||||||||||||| |||||||||||||| || ||||||||||||| ||| || |||||| | | ||||||| || ||| || ||||||| |||||||| ||| ||||
ACGAAAATGATGATGAGCAACCTAAGAAAAAGATCAGAATGGGGATGCCGGCAACTCAGTGGATTAGTGTCTACAATGCCCGTCGACCTATGAAACAGAGgtcagcatgatgcacatatctgcataatggcagtaacatgaattttccattgtcttgccacatttgtttatcag

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 11
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcacagtaatctgcttggtagcagtaaaataatactctattgtctgaccacat-----ttatttttcag-----
| || ||||| || ||||| || || ||| || ||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| || |||| | | | || | || | || | | | |||| || | | |||| ||| |
AAGAAGATGATGATGAACAACCAAATAAGAAGGTTCGAATGGGAATGCCTGCTACACAATGGATTAGTGTTTACAACGCTCGTCGGCCAATGAAGCAAAGgttttcttctgatattaaataagtttttgcaagtgattttaaaaatgtcagagcctaaaggtattatcttttggtgtag

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 11
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcacagtaatctgcttggtagcagtaaaa-----taatactctattgtctgaccacatttatttttcag----
| || ||||| || ||||| || || ||| || ||||||||||||| || || || ||||||||||| |||||||| ||||| |||||||| || |||| | | | || | || | || | ||| | | | || | ||| |||
AAGAAGATGATGATGAACAACCAAATAAGAAGGTTCGAATGGGAATGCCTGCTACACAATGGATTAGTGTTTACAATGCTCGTCGACCAATGAAGCAAAGgttttcttctgatattaaataagtttttgcaagagattttaaaatgtcagagcctaaaggtattatcattttgtgtag

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G21570.1 (Glycine max), 5'ss of exon 11
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcacagt---------aatctgcttggtagcagtaaaataatactctattgtctgaccacatttatttttcag------------------------
| || ||||| || || || || || |||||| | || || ||||||| |||||||||| ||||| |||||||| ||| | ||||||||||| |||||| | || | | || | ||| ||| || || || | | | || | ||
AAGAAGAGGATGATGAACAGCCCAAAAAGAAGATTCGTATTGGTTTGCCAGCATCCCAGTGGATAAGTGTTTACAATGCTCGTAGACCAATGAAACAAAGgtatactcccgtgtgacatgaagtttgttctgtatt--taatatgattctatttcaggcatttgaaattgatccatagggatggtaattgctcatttcccca

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 11
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcacagtaatctgcttg-------gtagcagtaaaataatactctattgtctgaccacatttatttttcag------------------------
| || || || ||||| || ||||| ||| | | ||||| ||||| || || || ||||||||||| |||||||| ||||| || ||||||||||||||| | || | || | | | || | | ||| || | || ||| |
AAGAAGAGGAAGATGAGCAGCCGAAGAAGAAGGTCCGTATGGGGATGCCTGCAACACAATGGATTAGTGTTTACAATGCTCGTCGACCTATGAAACAGAGgtatattaatgttggtcattcatcatgccatacctggaggatgttgtgggactgtgaaactattttggctttcttgctttgtgcccctattgtctttcct

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 11
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatg-----------gcacagtaa--tctgcttggtagcagtaaaata-atactctattgtctgacca-catttattttt-cag
|| || ||||| |||||||| ||||| ||| | ||||||||||||| || || || ||||||||||| |||||||| |||||||| ||||| || ||||||| || | ||| ||| | || | | | |||| ||| | | || | |||||| | || ||
AGGAGGATGATGATGAGCAACCAAAGAAGAAGGTCCGAATGGGAATGCCTGCAACACAATGGATTAGTGTTTACAATGCTCGTCGGCCTATGAAGCAAAGgtatgtgctttgagttacatattaagttcttcctgtttactgcaaaagggataaaaaggtttatgtttaacatttactgttgtag

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|29645032|gb|CB650039.1|CB650039
EST:     GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAG                         ATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
genomic: GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcaca ... tatttttcagATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
EST: gi|29645031|gb|CB650038.1|CB650038
EST:     GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAG                         ATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
genomic: GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcaca ... tatttttcagATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAG                         ATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
genomic: GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcaca ... tatttttcagATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
EST: gi|58668884|gb|CK057570.1|CK057570
EST:     GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAG                         ATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG
genomic: GCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcaca ... tatttttcagATACCACTACAATGTAGCAGATGATAGATTAGCACCACATATTCAAAAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTGAAGATGAGGAGCAACCTAAGAAAAAGATTAGAATGGGAATGCCAGCGACCCAGTGGATTAGTGTGTACAATGCCCGTCGGCCAATGAAACAGAGgtatggcacagtaatctgcttggtagcagtaaaataatactctattgtctgaccacatttatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA