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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTCCGTGCGATTCGAAGCATTCTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttccttctcatccgtatgtggtagtattttcaaggtcacatgaacattaaatatgaaatcaggtatatacagaaaacatctcgtattgactgtc...

Basic information

species Oryza sativa
transcript LOC_Os02g53210.4
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53210.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G046407_T01 (Zea mays), 5'ss of exon 7
ATTTTCCGTGCGATTCGAAGCATTCTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttccttctc--atccgtatgtggtagta----ttttcaaggtcacatgaacattaaatatgaaatcaggtatatacagaaaacatctcgtattgactgtc
|||||||||||  | || |||||| ||||||||||||||||||||||||||||||| || ||||| || || |||||   ||  |  ||  |  | | ||      ||    ||   ||| ||  | |||||||||||   ||||||     | ||        | |  | | || |   
ATTTTCCGTGCACTACGGAGCATTTTGTATGGTTTTGTTGCCTTCTTTTCAACATGTAATAGGCACCGACTCAGgtattttttttattccaacacctgtgcaacgatacagtttagtaagatccgaggaacattaaatg-aaaatcacaatgacaccttg---gtttactgtggagtt--

upper sequence: LOC_Os02g53210.3 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv12s0059g01300.t01 (Vitis vinifera), 5'ss of exon 8
ATTTTCCGTGCGATTCGAAGCATTCTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgta-------accttccttctcatccgtatgtgg---tagtattttcaaggtcacatgaacattaaatatgaaatcaggtatatacagaaaacatctcgtattgactgtc
 ||||||| ||  || |||||||| |  ||||||| |||||||||||  || | |||||||| ||||||||||||||       |  ||  || || |  | || |     |   ||  | |   |    ||     | | | |    | |  | |  |   |||| || || ||         
GTTTTCCGGGCTGTTAGAAGCATTTTAAATGGTTTCGTTGCCTTCTTCACAGCCTGCAACAGACATCGGCTTAGgtatgctataattttatttttcctttgcatttcaatctgccatagttatttttgtctgtctgctcattttcttcttaatttttaatgaaaaatatatc-ta---------
















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|29674942|gb|CB671217.1|CB671217
EST:     CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
EST: gi|87031749|gb|CI272450.1|CI272450
EST:     CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
EST: gi|38482043|gb|CF966104.1|CF966104
EST:     CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
EST: gi|33692950|gb|CF321189.1|CF321189
EST:     CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
EST: gi|58693404|gb|CK082091.1|CK082091
EST:     CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
EST: gi|86827594|gb|CI272900.1|CI272900
EST:     CTGTATGTTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
EST: gi|58600474|gb|CK011002.1|CK011002
EST:     CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAG                         CATTTACAAGCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC
genomic: CTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttcc ... catgctgcagCATTTACAACCACATTCAAGTATTTCTCCGACGCCTATCTCGTGTTTTAAC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTCCGTGCGATTCGAAGCATTCTGTATGGTTTTGTTGCCTTCTTTTCAACATGCAACAGGCATCGGCTTAGgtaaccttccttctcatccgtatgtggtagtattttcaaggtcacatgaacattaaatatgaaatcaggtatatacagaaaacatctcgtattgactgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaca