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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g18310.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttca-------aattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
       ||   |||  ||| | || |||   |||| ||   ||  | |  |||        || ||    |||||||||| | | |    | |||||  ||||||||||||| | |||||||| ||||||||||||||||| ||||| |||||||| || || ||||||||||||||||||||||||||||||||||||||||||
-------agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 7
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattct-----agGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
    ||   ||    | |||||  |   |  ||| |   |  ||| ||   ||    ||      | |  |  | | |||   || | ||    || |     |||| ||  |||||||  | ||||| || || || || ||||| |||||||| || ||||| |||||||||||| | || ||||||||||||||||| |||
---ctggcaaaaatgtcatttccatttgta-gttcatcaaagttagtaaatttggttttttaaaagtaaattatttttaatt-ttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
--catatgaagaatgaataatttctgtc---aatgtgttgaaat-actttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
   ||   || ||||    |||||  ||   | |   |  || | | |  || ||  || |||  |    |  | || ||   |||    | |  ||      ||||| ||  ||||||| || ||||| || || || || ||||| |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatg------tagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
-----catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
        |  || ||||    ||| |  ||  |  ||| |  || |||| ||   |  ||| ||  |||| |  |      |  |  | ||          |||||  | ||||||||||| || ||||| |  || || ||||| || ||||| || |||||||||||||||||| | || ||||||||||||||||| |||
tacctggaaaaaaaaatgccacattcccatctgta-gttcatctaatttagtaaaat--aaaata--tttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagt---tcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
 |  || | ||  |||      |  |  | |||      |  |||||  |    | |  |  |||| | |   |  | | |||| |  ||       |  |||||  | ||||||||||| || ||||| |  || || ||||| |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||
tacctggaaaaaaaatgccacattcccttctgt-acttcatcttatttagtaaaataaaatatttgaaatgaataatttctaacta--gtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
catatgaagaatgaataatttctgtc---aatgtgttgaaatactttattatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
    ||   ||    | |||||  |    | |   |  || |   | | | || ||      |  |      || ||   |    | |    |     | ||||| ||  |||||||  | ||||| || || || || ||||| |||||||| || ||||  |||||||||||| | || ||||||||||||||||| |||
---ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttactaatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
--catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagttctt--ctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
   |  |  || |  |  |  ||   || || ||||| |       |||    | | ||||   ||   | |   |   |||||| | | |      |||  ||||||| ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||| ||||| |||||||| || |||||||||||||||||||||
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaattta----tatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
---catatgaagaatgaataattt--ctgtcaatgtgttgaaatactttattatgct-tcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
     |   |  | || ||  ||   |    |||||| |      |    | | ||| | ||  |||  | | ||||       ||  | | |       ||  |||||||||| || |||||||| ||||| || || || ||||| || || || ||  | || |||||||||||||| || || |||||||||||||| |||
tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttg------aatgagtctctgatggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG

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|58689570|gb|CK078257.1|CK078257
EST:     CTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG                         GTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGG
genomic: CTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttca ... gccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGG




















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: 52 (upstream exon), 64 (downstream exon)
Score: 4

GACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTGgtacttttca ... gccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcttcaaattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
                             ctgtaac  putative branch site (score: 4)
                                              ccattct  putative PPT
      ttcaaatta  TA-rich tract