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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctagtttgtatatatttccttggagttctcagtgcagttacacacatttctggtggtagaataatctaacagttcttttttgggttaattggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAATGAG

Basic information

species Oryza sativa
transcript LOC_Os05g07130.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 8
-cttctagtttgtatatatttccttggagttctcagtgcagttacacacatttctggtggtagaataatctaacagttcttttttgggttaattggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAATGAG
 ||  | | || |  |||      |      ||  |  |||| | ||  || ||  ||  ||||   || ||||| || ||||     || || || |||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||
cctgttggattttcaataccattatctgagcctacgc-cagtaaaactaatatcctgttctagagcgatgtaacattttttttgcatttttatcggctcagTCTGCAGATTTTTTCCGTGATGATAATCCTGAAGGTATTGAGGCACGTAATGAG
















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|33381245|gb|CF196588.1|CF196588
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
EST: gi|29616051|gb|CB621063.1|CB621063
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCT
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCT
EST: gi|58695801|gb|CK084488.1|CK084488
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
EST: gi|84117327|gb|CD151094.1|CD151094
EST:     GTACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGTAAT
genomic: GTACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
EST: gi|29616011|gb|CB621023.1|CB621023
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGAT
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGAT
EST: gi|29615974|gb|CB620986.1|CB620986
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCTG
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTG
EST: gi|58688458|gb|CK077145.1|CK077145
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGTAAT
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
EST: gi|29612781|gb|CB617794.1|CB617794
EST:     TACCGCCGCCTGAAGCATGGAGCAAATCAG                         TCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT
genomic: TACCGCCGCCTGAAGCATGGAGCAAATCAGgtactaataa ... attggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatttctggtggtagaataatctaacagttcttttttgggttaattggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAATGAG
                 aataatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctagtttgtatatatttccttggagttctcagtgcagttacacacatttctggtggtagaataatctaacagttcttttttgggttaattggttcagTCTGCAGATTTTTTCCGTGATGATAACCCTGAAGGGATTGAGGCACGCAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - -tgcagtt
- - - - - - - - - - - - - - - - - - - - - acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - ctggtgg