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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctggaagaaacaaaacatatatgattcattttcacctaaattgccattgttttgtgagtttcttgctctggtaatttattgtcctcatctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTAGATCAATTCAAATGTGAA

Basic information

species Oryza sativa
transcript LOC_Os02g12810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12810.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G413069_T01 (Zea mays), 3'ss of exon 5
-aagctggaagaaacaaaacatatatg-attcattttcacctaaattgccattgttttgtgagtttcttgctctggtaatttattgtcctcatctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTAGATCAATTCAAATGTGAA
| |||| | | | || || || | | || | | | | | || ||||||| ||| | || | || |||| | ||| ||||| ||||||||||||||||||||||||||||||||||| |||||| ||||||| ||||| |||||||||
tcacctggccaattctgttgttgaatatatgcagtcttcccatgacttctgattctctgggagtttcc-attctcctgatgttttttcct-gtaaatttcagGAGGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCAGGTGTTTCACTAGAGCAATTTAAATGTGAA

upper sequence: LOC_Os02g12810.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G34730.1 (Glycine max), 3'ss of exon 6
----aagctggaagaaacaaaacatatatgattcattttcacctaaattgccattgttttgtgagtttcttgctctggtaatttattgtcctcatctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTAGATCAATTCAAATGTGAA
||| || | | | | ||| | || | ||| | | || | | || || ||||| || | | |||| |||| | || ||||||||||| || ||||| ||||| ||||| ||||| || |||| |||||||| ||||||||||| |||
tgggaagatgaa--gatctcattatacaagacttgctttgattgtgagtgaaagtacttagt-agtttttttgtgcactgattt-ttgtaatttggcatgacagGAAGTTGCTGTAAAGAAGTTTCTGGACCAAGATTTCTCTGGTGATGCACTAGCTCAATTCAAATCCGAA
















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|33796224|gb|CF323978.1|CF323978
EST:     GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACT                         GAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTNTATCGGGTGTTGCACT
genomic: GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACTgtaagtcaca ... tctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATT-TATCGGGTGTTGCACT
EST: gi|29623119|gb|CB628130.1|CB628130
EST:     GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACT                         GAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
genomic: GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACTgtaagtcaca ... tctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
EST: gi|58594152|gb|CF992460.1|CF992460
EST:     TTGGTCTAGGTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACT                         GAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
genomic: TTGGTCTAGGTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACTgtaagtcaca ... tctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
EST: gi|33793152|gb|CF322457.1|CF322457
EST:     GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACT                         GAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
genomic: GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACTgtaagtcaca ... tctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
EST: gi|29639858|gb|CB644867.1|CB644867
EST:     GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACT                         GAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
genomic: GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACTgtaagtcaca ... tctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
EST: gi|112785946|gb|EE591740.1|EE591740
EST:     GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACT                         GAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA
genomic: GTTCATATGGGGAAGTATATCATGCAGATTGGAATGGCACTgtaagtcaca ... tctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccattgttttgtgagtttcttgctctggtaatttattgtcctcatctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTAGATCAATTCAAATGTGAA
                                       tcctcatct  CT-rich tract
 taatttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagctggaagaaacaaaacatatatgattcattttcacctaaattgccattgttttgtgagtttcttgctctggtaatttattgtcctcatctattgcagGAAGTTGCAGTGAAGAAATTTCTTGACCAGGATTTATCGGGTGTTGCACTAGATCAATTCAAATGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA