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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCTGCATGGCTGTCAGAAGAAGACATTTCCTACTATGCCGAGAAATTTGAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctcttggttatacagttcattgttttattcatccttcattgctgttaagtgaggaaagcaacatgatattgtttagcattgtacagggaaagtc...

Basic information

species Oryza sativa
transcript LOC_Os01g15120.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15120.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G161658_T01 (Zea mays), 5'ss of exon 3
GCCCTGCATGGCTGTCAGAAGAAGACATTTCCTACTATGCCGAGAAATTTGAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaatt--ctcttggttatacagt--tcattgttttattcatccttcattgctgttaagtgaggaaagcaacatgatattgtttagcattgtacagggaaagtc
| ||| ||||||| ||||| ||||| ||||| |||||||| || ||||||| ||| || || |||||||||||| | ||||||||||| |||||||||  |||  |  ||  |||| |  ||    |  |  |||      | ||| |||| ||  |           | |    | | | |   |  || ||   |  |    
GTCCTCCATGGCTATCAGAGGAAGATATTTCTTACTATGCAGAAAAATTTGCGAAAACAGGCTTTACTGGAGGACTTAACTACTACAGGTGCATAGACAGgtatgtgccttctggtcagtcaacaattttgatttcgcattttctttattgatgcaatcaatcatttaccatccaacaatttcctgttttttatttgcca----
















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|88968460|gb|CI098702.1|CI098702
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88268988|gb|CI380286.1|CI380286
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAAGCTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGA
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAA-CTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGA
EST: gi|86539720|gb|CI179926.1|CI179926
EST:     TACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: TACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88904034|gb|CI006267.1|CI006267
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|218495743|gb|FG944638.1|FG944638
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATTAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88288082|gb|CI512759.1|CI512759
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|86538738|gb|CI178944.1|CI178944
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88841456|gb|CI005536.1|CI005536
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|86538746|gb|CI178952.1|CI178952
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGATCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88691185|gb|CI735264.1|CI735264
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|58688475|gb|CK077162.1|CK077162
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|86539805|gb|CI180011.1|CI180011
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|29686898|gb|CB683173.1|CB683173
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|86257420|gb|CI004237.1|CI004237
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|15853006|gb|BI805802.1|BI805802
EST:     TACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAGAAAGTTCCGA
genomic: TACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATA-AAAGTTCCGA
EST: gi|88688202|gb|CI731778.1|CI731778
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88559946|gb|CI490566.1|CI490566
EST:     TTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: TTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88464489|gb|CI544950.1|CI544950
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|3763601|gb|AU030353.1|AU030353
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|86540535|gb|CI180741.1|CI180741
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88544606|gb|CI472720.1|CI472720
EST:     TGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: TGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88455049|gb|CI516687.1|CI516687
EST:     TTGAAGTAGTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: TTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88435812|gb|CI513951.1|CI513951
EST:     GACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
EST: gi|88689305|gb|CI732881.1|CI732881
EST:     GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTT                         GAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC
genomic: GAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 75 (downstream exon)
Score: 48

GCCCTGCATGGCTGTCAGAAGAAGACATTTCCTACTATGCCGAGAAATTTGAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctct ... gttcatgcagGAACTGGGAGCTGACTGCACCATGGACTGGAGTTCCAATAAAAGTTCCGACAAAATTCATCGTTGGAGATCAGGACCTTACGTACAACATTCCAGGTGTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCTGCATGGCTGTCAGAAGAAGACATTTCCTACTATGCCGAGAAATTTGAGAAGACTGGATTTACTGGAGGATTGAACTACTACAGATGCATAGACTTgtaattctcttggttatacagttcattgttttattcatccttcattgctgttaagtgaggaaagcaacatgatattgtttagcattgtacagggaaagtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG