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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattattccagtgattttgtgattcccattggctcatgttgttcgacttgatttcacttctagactcaggcaacttgcctgggactaaaaactgttgtttgaaacttccattttgattatttgacattcttttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os06g01410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 6
gtaattattccagtgattttgtgattcccattggctcatgttgttcgacttgatttcacttctagactcaggcaacttgcctgggactaaaaactgttgtttgaaacttccattttgattatttgacattcttttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG
                                                     || |  ||||     |  |  | |    | ||  | |||  | || ||     |||  ||  |||  |      ||| ||||  ||||||||||||    |||||||| || ||||| | |||| ||||||||||||||||||| |||||||||||| | |||||||| ||||||||||||||||||
----------------------------------------------------gttactattctttctgcttgatattctattagggtttaaatttcttttt-----cttttatgctgacca------atttttttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG

upper sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G29760.2 (Glycine max), 3'ss of exon 6
-gtaattattccagtgattttgtgattcccattggctcatgttgttcg-acttgatttcacttctagac--tcaggcaacttgcctg-ggactaaaaactgtt--gtttgaaacttccattttgatt--atttgacatt----cttttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG
  |  |   |||| |||  || | |||||  |    |||   | |  |  |   |  ||| | ||| ||  |   |   |  || |    |||  | | |  |  || |     || |||||| ||   | || |||||      |||  || |||  |    | |     |||  | ||| | | | || |||| | | |||| |||||| ||||||| ||||| |||||||| ||||||||||| |    |
gtttgtctgtccaatgaagttct-attcctttcctttcaccatttatgtgcaaaacctcattcctaaacctttttgtgtccagctttcaaacttgacaatacttagtgtttgctttgcattttcatggaacttaacattgccctctttcctgtagTTGTATCAAAACAAGTTGTCTACTATAAGGGTCATCAAGTACACAATCTCAATGAATTGGAATACATAAATGGTGAAGTCTGGGCAAATGTTTTTATG

upper sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G24450.1 (Glycine max), 3'ss of exon 6
-----gtaattattc--cagtgattttgtgattcccattggctcatgttgttcgacttgatttcacttctagactcaggcaacttgcctgggactaaa------aactgttgtttgaaacttccattttgatt-atttgacattct----tttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG
       ||||      || |||  ||   |||||  |    |||   | ||   |   | ||   || | |   |||    ||  | ||  | ||        |  |  ||| |    ||| ||||||  |  | || |||||      |||  || ||   |    | |     |||  | ||| | | | ||||||| | | |||| |||||| ||||||| ||||| |||||||| ||||||||||| |  | |
gtttgccaattgcctgtcaatgaagttcc-attcctttcctttcaccattttttcccaaactt---ttttgggtccagttttctaacttgacaatactttgtttagttaatgtgtatgccttgcattttagtggaatttacattgccctattttctgtagCTGTATCAAAACAAGTTGTCTACTATAAGGGTCATGAAGTACACAATCTCAATGAATTGGAATACATAAATGGTGAAGTTTGGGCAAATGTTTTACCG

upper sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 3
-gtaattattccagtgattttgtgattcccattggctcatgttgttcg-acttgatttcacttctagactc-----aggcaacttgcctg-ggactaaaaactg--ttgtttgaaacttccattttgatta--tttgacatt----cttttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG
  |  |   |||| |||  || | |||||  |    |||   | |  |  |       || | ||| ||        | |  | ||| |    |||  | | ||  |||| |     ||  |||| ||| |   || ||| |      |||  || ||   |    | |     |||  | ||| | | | || |||| | | |||| |||||| ||||||| ||||| |||||||| ||||||||||| |    |
gtttgtctgtccattgaagttct-attcctttcctttcaccatttatgtgcaaagccccattcctaaacctttttgggtcgtcctgctttcaaacttgacaatgctttgtgtttgctttgaatttagatgaaacttaacactgctctcttttctgtagCTTTATCAAAACAAGTTGTCCACTATAAGGGTCATCAAGTACACAATCTCAATGAATTGGAATACATAAATGGTGAAGTTTGGGCAAATGTTTTTATG

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|88357314|gb|CI622163.1|CI622163
EST:     CAGTGATGGTACTTCAAGGTTATACCAGCTTGATCCAAAGTCAATTCAAG                         TCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTA
genomic: CAGTGATGGTACTTCAAGGTTATACCAGCTTGATCCAAAGTCAATTCAAGgtaattattc ... tttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTA




















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: 59 (upstream exon), 64 (downstream exon)
Score: 23

AAAATGAGTGATGGGTGGGGGTTGGCTACTGATGGAAAAGTTCTTTTTGGCAGTGATGGTACTTCAAGGTTATACCAGCTTGATCCAAAGTCAATTCAAGgtaattattc ... tttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaactgttgtttgaaacttccattttgattatttgacattcttttggtgcagTCATGAAGACAGTGACTGTGAAATATCAAGATAATGAAGTCCCCTATCTTAATGAACTGGAATATATAAACGGTGAAGTATGGGCAAATGTCTGGCAG
                                       cattctttt  CT-rich tract
                        attttgattatttga  TA-rich tract