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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgataaagacacactgttcttttgaccagcataataaagataaactgtatgttgtagcttgtgtaatcctaacaaagataatctgatatgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAATATTGGAAGCTGCTGCGATAGCTAGGCTTGGAGTTGATGTGTATATTAC

Basic information

species Oryza sativa
transcript LOC_Os01g55890.6
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55890.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G424873_T02 (Zea mays), 3'ss of exon 10
catgataaagacacactgttcttttgaccagcataataaagataaactgtatgttgtagc-ttgtgtaatcctaacaaagataatctgat------atgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAATATTGGAAGCTGCTGCGATAGCTAGGCTTGGAGTTGATGTGTATATTAC
   || || ||    |   |    ||       |  |     |||||||  || |||||| |||| |  |    |  |||||| |||| |      ||| | ||||||||||||||| || || |||||||||||||| || || ||||||||||||||| |||| ||||| | |||||||||||||||| | || |||||||||||
---gacaatgatgtgc--ctggcctggttttttttttcttc-taaactgcttgctgtagccttgtattttgtagagtaagata-tctgttgttctcatgtactgcagTGGAGATATCAGTTGCAGCACATGACACCACCGGTGGGATGGAGACCAAAATACTGGAGGCTGCAGTGATAGCTAGGCTTGGAATAGACGTGTATATTAC
















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|88376340|gb|CI533242.1|CI533242
EST:     GCATTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: GCATTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
EST: gi|87019242|gb|CI279752.1|CI279752
EST:     TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
EST: gi|88255259|gb|CI354083.1|CI354083
EST:     AGGCAACAAGAAAGGAG                         TGGAGATATCTTTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: AGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
EST: gi|89167691|gb|CI021390.1|CI021390
EST:     TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
EST: gi|86883806|gb|CI328772.1|CI328772
EST:     CCAGCATTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCTCATGACACCACTGGCGGAATGGAGACCAAAA
genomic: CCAGCATTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
EST: gi|88838193|gb|CI372761.1|CI372761
EST:     TTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: TTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACC-AAA
EST: gi|86833007|gb|CI333606.1|CI333606
EST:     TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
EST: gi|58585715|gb|CF984023.1|CF984023
EST:     TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAG                         TGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA
genomic: TGGCAGCTGGTCGATTGTAAAACCAGCATTGAAAGGCAACAAGAAAGGAGgtataattta ... tgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtatgttgtagcttgtgtaatcctaacaaagataatctgatatgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAATATTGGAAGCTGCTGCGATAGCTAGGCTTGGAGTTGATGTGTATATTAC
                              aaagataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgataaagacacactgttcttttgaccagcataataaagataaactgtatgttgtagcttgtgtaatcctaacaaagataatctgatatgcattgcagTGGAGATATCTGTAGCTGCACATGACACCACTGGCGGAATGGAGACCAAAATATTGGAAGCTGCTGCGATAGCTAGGCTTGGAGTTGATGTGTATATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG