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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatatgttcttagccaactggtttatgcatactgccttgtcgtaaagtgcatagtttatctaatttatctggatttagtgatacaactctgtggactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG

Basic information

species Oryza sativa
transcript LOC_Os07g31460.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G474236_T01 (Zea mays), 3'ss of exon 3
gtaa-aatatgttcttagccaactggtttatgcatactgccttgtcgtaaagtgcatagtttatctaatttatctggatttagtgatacaactctgtggactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG
|||| ||| || |  |  ||||||| ||| |||||| |||  ||                | | ||||          ||| |  |    |  ||||     ||  ||||||||||||||  || ||||||| ||||| ||||| |||||||||||||| || |||||||||||||||||||||||||||||||||
gtaataatttggttctgcccaactgatttctgcatattgcactgcg--------------tcacctaa--------agttttgcaa----atgctgt----cttttagGTGGAACAAGAAGTTAAATTATGTTATTGCGATTTCTAAAGATGGAGTACGGGACGTAACAAAACGCTACACCAGAAAGTGGCATGAG

upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA19G43320.4 (Glycine max), 3'ss of exon 11
----------------------------------gtaaaatatgttcttagccaactggttta---tgcatactgccttgtcgtaaagtgcat----agtttatctaatttatctggatttagtgat-acaactctgtggactttcc-----agGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG
                                  |||     || | | | ||| ||  || |   ||   |     ||||  |      |||    ||||||  |  |   ||    |||  | || |  | | | |  | |||       ||||||   || |||||| |||||||||| || ||  |||||||||||||   |||||| || ||||| ||||| || ||||||||||||
gtattattcatttatgcagtactttcactttactgtattcattgctatcatccatctaattgaaagtgagaaaatagttgttcttgtcctcattaggagtttacatcttgcttccatgtttcctcattattatttttttaaatttgtggcatagGTGGGGGAAAAAACTAAATTATGTAATAGCCATAGCAAAAGATGGAGTTTATGATGTCACCAAACGATACACAAGGAAGTGGCATGAG

upper sequence: LOC_Os07g31460.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv14s0030g01930.t01 (Vitis vinifera), 3'ss of exon 11
-------------------gtaaa-atatgttcttagccaactggtttatgcatactgccttgtcgta-aagtgcatagtttatctaatttatctggatttagtgatacaactctgtggactttcc---agGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG
                    |  | |||| |  | |   | ||  |   ||  |       | | | | || |   |    | |  | ||| || | ||| | || |  |||    |    ||||    || |||||||||||| |  ||||| ||||||||||  |||||||||||||   |||||| || ||||||||||| |||||||||||||||
gtacttctctgtcacagatatggatatatttcttgaattatctcttcattgtttttcttaatcttggacaaatcttttagctctgaactttctcagtattaaatg-tttaacctcatactttttcttaaagCTGGAACAAGAAATTGAATTATATAATTGCTATCGCAAAAGATGGAGTTTATGATGTCACTAAACGCTACACAAGAAAGTGGCATGAG

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|29643983|gb|CB648990.1|CB648990
EST:     CTAGATCCATGTGAAGGAGTCTATGATAATCCCCTATTGTATGAGAAAGG                         GTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACG
genomic: CTAGATCCATGTGAAGGAGTCTATGATAATCCCCTATTGTATGAGAAAGGgtaaaatatg ... gactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACG
EST: gi|29678551|gb|CB674826.1|CB674826
EST:     CTAGATCCATGTGAAGGAGTCTATGATAATCCCCTATTGTATGAGAAAGG                         GTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACG
genomic: CTAGATCCATGTGAAGGAGTCTATGATAATCCCCTATTGTATGAGAAAGGgtaaaatatg ... gactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACG
EST: gi|58696150|gb|CK084837.1|CK084837
EST:     CTAGATCCATGTGAAGGAGTCTATGATAATCCCCTATTGTATGAGAAAGG                         GTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACG
genomic: CTAGATCCATGTGAAGGAGTCTATGATAATCCCCTATTGTATGAGAAAGGgtaaaatatg ... gactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatagtttatctaatttatctggatttagtgatacaactctgtggactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG
         atctaat  putative branch site (score: 3)
                                               ctttcc  putative PPT
      tttatctaatttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatatgttcttagccaactggtttatgcatactgccttgtcgtaaagtgcatagtttatctaatttatctggatttagtgatacaactctgtggactttccagGTGGAACAAGAAACTAGATTATGTAATTGCTATTTCAAAAGATGGAGTACGTGATGTAACAAAACGCTACACCAGAAAGTGGCATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA