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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcttatttacataagtatcaggccgtcatgtgcgaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattcatgcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 6
gtgagtcttatttacataagtatcaggccgtcatgtgcgaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattcatgcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT
                                 || |     |||  ||  |  ||  |  |||    | |    |   | |   ||   | ||||||  ||   | ||      ||| ||||||||||| || ||||||||||| |||||||||||||||||||||||||| |||||||||||||||| ||  |||||| | | |  ||||||||||||||
--------------------------------gtgagtctc-tgttacagtttacacatgcatgcacatatctgcatcctatc--agtatctatctaatgtttggattttcgctcttttcagCCTGATACGGTTACAGGAGACATTGTTTTTGTCTTGCAACTTAAAGACCATCCAAAATTTAAGAGGATGTACGATGACTTATATGTTGAGCACACAATCT

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G27030.1 (Glycine max), 3'ss of exon 6
gtgagtcttatttacataagtatcaggccgtcatgtgcgaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattcatgcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT
|| |||  | | ||  || ||||   | | |        | |  | | ||        ||| | ||   ||| |||||   ||||   ||  |  |||   |||| ||  |   | ||||||||||| ||| | ||||||||||| |||||||| |||||| | || || |||||||| || |  ||| ||   |||||||||| || ||| ||||   || 
gtaagtggtttata-gtatgtat---gtcatttgtcttaatactttgtaa-----ggattgct-tggaagttgataatt--ttggccttcttaattaa--atgcatatgtac-ttgttgcagCCTGACACAATCACAGGAGACATTGTTTTTGTATTGCAAGTAAAGGATCACCCAAAGTTCAGAAGGGAGCAGGATGACCTCTATATTGATCACAATCTCA

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtcttatttacataagtatcaggccgtcatgtgcgaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattcatgct-tttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT
                         || |    | |     ||   |    ||   | ||    |      || |||||| ||   |        ||  |   |   ||||||   |||||||||||||||  | || |||||||| |||||||| |||||||| || |||||  | || || ||| |||| | ||| || ||||     ||||| ||  || 
----------------------cagggtcaatttatatttcatcatgtttttcatctttttggatagacactcttaatatttttagggatgacaatagtaaccctg-ttcatgtcatttgcagCCTGATACGATTACGGGAGACATTGTTTTTGTGTTGCAACTGAAGGACCATGCCAAGTTCAAGCGGAAATATGACGATCTCTACGTAGAGCATACCCTCA

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S174_37V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------gtgagtcttatttacataagtatcaggccgtcatgtgc----gaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattca---tgctt-ttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT
                                                  ||     || ||   |  || || | ||    |||||     | | |||   |      |  || |||| | |  |   || ||| ||  | |   ||   |  |||     ||    || || |||||||| || ||||||||||||||||| || || || |||||||| || || ||||| || || ||||||||    ||||| || |||   ||||| ||  |  
gtgcgttactctccgtgcgttcaaggcgtgctcttctgacaacaaatttcgtagaagtttttgtgaacaggataacgcttggatgtgtatatggattgtctgatacgaaaagttaatgt-tattctggaaacatgctgacggttagattgcattttgtgtgatcgatgtgtttgttgcagCCCGACACAGTGACAGGAGACATTGTATTCGTTTTGCAACTGAAGGAGCACCCGAAGTTCAAGAGGAAAGGGGATGATCTGTTTGTGGAGCATACTTTGA

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|218492553|gb|FG956401.1|FG956401
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|58661241|gb|CK049921.1|CK049921
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTA
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTA
EST: gi|29665502|gb|CB661777.1|CB661777
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAG
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|218503180|gb|FG945924.1|FG945924
EST:     AATGCAACATGGCCAAAAGATTGTATTCCAGGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: AATGCAACATGGCCAAAAGATTGTATTCCA-GGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|396941261|gb|HO188470.1|HO188470
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|58667485|gb|CK056171.1|CK056171
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|218484817|gb|FG946762.1|FG946762
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGTGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|33795096|gb|CF323421.1|CF323421
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|29686473|gb|CB682748.1|CB682748
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|29627564|gb|CB632575.1|CB632575
EST:     GCTGATGAAGCT                         CTTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|58603501|gb|CK014029.1|CK014029
EST:     AATGCAACATGGCCAAAAGATTGTATTCCAGGGTTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: AATGCAACATGGCCAAAAGATTGTATTCCAGGGT-GAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|218485257|gb|FG950272.1|FG950272
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTATTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|29665503|gb|CB661778.1|CB661778
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|33797209|gb|CF324468.1|CF324468
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGG
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGG
EST: gi|218482248|gb|FG968976.1|FG968976
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|58604823|gb|CK015351.1|CK015351
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|3767212|gb|AU031322.1|AU031322
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|29686472|gb|CB682747.1|CB682747
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|116875639|gb|EC366147.1|EC366147
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|14571405|gb|BI118773.1|BI118773
EST:     GAATGCAATATGGCCAAAAGATTGCATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|3763799|gb|AU030551.1|AU030551
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|218499207|gb|FG956931.1|FG956931
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
EST: gi|29683464|gb|CB679739.1|CB679739
EST:     GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC
genomic: GAATGCAACATGGCCAAAAGATTGTATTCCAGGGTGAAGCTGATGAAGCTgtgagtctta ... gcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttcataatatgttggagctcccatctaacattgcaaattcatgcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT
                         atctaac  putative branch site (score: 2)
                                            tgctttt  putative PPT
      ataatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcttatttacataagtatcaggccgtcatgtgcgaaatgtggcaactcgcatcttgatgtgtgtgttcataatatgttggagctcccatctaacattgcaaattcatgcttttgcagCCTGATACAGTGACAGGAGACATAGTTTTTGTCTTGCAACTTAAAGACCACCCAAAATTTAAGAGGAAGTTTGATGACCTCTTTACTGAGCACACAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA