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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

Basic information

species Oryza sativa
transcript LOC_Os05g34830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
-----------gtacgtctcttccatctccctcctccatcc-atgcaaacttatagctactgttcatcgatcgtccatgactc----------catgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
             |  |   |  |||    ||     |    ||   ||||| |   || || | |   ||     ||                ||| |||||||||  ||||||| ||||| |||||||| || ||| | ||  |||||||||||||||||||||| ||||||||||||||  |||| ||| |||| ||
taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
gtacgtctcttccatctccctcctcc-atccatgcaaacttatagctactg-ttcatcgatcgtcca---tgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
    ||  | |  |||| |  | ||  ||  || |  | |  ||  |  |  |||||  ||  |      ||      | ||||| ||||    ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| ||  |||||||||| || || ||  |||| ||
----gtaacatt-atcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 1
-----gtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttca-tcgatcgtccatgactcc----atgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
      |   | ||||            |   |   ||||| || || || |  ||||| | ||| |   |||| |      |||||| ||| |     ||||||||||| || ||||||||||| || |||||||| || || ||||||||||| || ||||||||||| ||||||||   ||| ||
gttcgtttaatttcttatggggtttcgttttgtgactgcaa-ctaattgc-atagttcaattgattgataatgagttggatgatgcagAAATTGGCTACTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGATCGGAAATACCCGAACGGTTCACGGCCGAACCGTGCCGCCGGAAGCGGCTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G32850.1 (Glycine max), 3'ss of exon 1
--------------------------------------gtacgtctcttccatctccctc-----ctccatccatgcaaacttatagctactgttcatcga-------tcgtccatgactccatg--cagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
                                       |  | || ||  |  | | |      ||  || |    | | || |     ||   | |  |       |  |  |||  |  |||  |||  ||||| || ||||| ||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| ||| | |||||||| || |||||   ||||||
gtacctttttttcttttctcactctagtctctgtattcttttgccttttttaatttcattagggtcttaattctactacattttttttctctccaccttaaagtcctattatttatgtttttatgtacagAGATGGCTCTTTACGGTGAGAAAGAGTGGTACTTTTTCTCTCCTCGAGACCGAAAATACCCAAACGGTTCGAGACCGAACCGGGCTGCCGGAAGCGGGTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
----------------gtacgtctc-ttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
                 |  || || ||   | |    ||     | ||   | | | ||| | |  || || |||  |   |   || |||||| ||| |   | ||||||||||| || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||||||||||||||   ||| ||
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagtt-caattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------------gtacgtctcttccatctccctcctcc---atccatgcaaacttatagctactg------ttcatcgatcgtccatgactc--catgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
                                                                                | ||   |||| ||      ||    ||  ||   |  || |   || |       || ||      |   || |     |||||||||||||  ||||||| ||||| |||||||| || ||| | ||  |||||||||||||||||||||| ||||||||||||||  |||| ||  |||||||
gtaacagtaatacacaaatcgaatccattatctttttttctctcctctgcgactttttttcgttttccttctctgctaaccatcagatccaccttataattctgaaatatataatatttttttattaataaataattttattttcttttggtgtcgtgttatgcagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGAACCGGGTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
---gtacgtctcttccatc--tccctcctccatccatg-caaacttatagctactgttcatcgatcgt--ccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
     |      |||  ||  ||  || | | || ||  |  | |  ||  |  | || ||  || ||  |  ||   |  | ||||| ||||    || || ||||| |||||||||||||| || || |||||||| || ||||| ||||| ||| |||||||||| || || ||  |||| ||
gtaacataatcattcattcattcattcattcttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
--------gtacgtctcttccatctccctcctcc--atccatgcaaactt-atagctactgttcatcgat-cgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
         |  |  ||||| |  |   |    |  |  ||||     |  | |     |||| || ||   ||   |  || | | |||  ||| | |||||||| ||||| ||||||||||||||||| ||| | || || || ||||| ||||| ||||| || ||||| || || ||  |||| ||
gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgtttgtt-cttctttcagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
-------gtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatg--cagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
        |  |||     ||       | |       ||  || | |     |   ||    ||   | |     |   |   ||| ||||||| ||||||| ||||| || |||||||||||||| | | | ||||| || ||||| ||||||||| | || ||||| || || ||  |||| ||
gtaaaacttcagtccacgacaagattgacatatggttttgtgaattgactttgagattttgaagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA

upper sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
------------------gtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtcca-----tgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
                        ||||   |     |||     | || ||||| ||  ||  ||||    | |||  |        ||  |   |||||||||||| |||||||| || |||||||||||||||||||| ||  |||||||||| || || ||||| ||  |||| ||||| || ||||| ||||| ||
aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttca-gcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

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: 75 (upstream exon), 41 (downstream exon)
Score: 11

GTGATGCACTACCTCTGCCGGCGGTGCGCCGGCCTCCCCATCGCCGTCCCCATCATCGCCGAGGTCGACCTCTACAAGTTCGATCCATGGCATCTCCCAAgtacgtctct ... ctccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA
           aaacttata  TA-rich tract