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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG

Basic information

species Oryza sativa
transcript LOC_Os03g61970.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053299_T01 (Zea mays), 3'ss of exon 3
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctct--------tcattggtgatatgacccca--------------gtgcgttgtggct---tgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
||| ||||||| ||||  || ||   ||  ||| ||| ||     || |||||        ||||||||||| ||||  ||               ||  | |   ||   ||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||| || ||||| || || |||||||| |||||| || ||||||||||||| ||
gcacgtgtccactttcacctcttattaa--agtttttctaggacaacgtctctgattctcgtcattggtgatctgacgacaccattctactacctatgtctcggtactctgtgtgcagGTATTGTGCTCGATTCTGGTGATGGTGTGACCCACACCGTGCCAATCTACGAGGGATACGCGCTCCCTCATGCCATTCTTAGGCTGGATCTTGCTGGCCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 3
-----------gcatgtgtccattttcta--ctattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
            || | ||    | |  |  |  ||| | || | | | ||  ||     || || | ||||||    |   |    |  |||| |  ||   |||||||||||||||||||||||||||||||||  ||||| ||||| || |||||||| ||||| ||||||||||| |||||||||||||| |||||||| ||
attccacacgtacaagagtgggatatacatgcatttctacattaat-tatgaccagcattatttccttattggt----ttgtcttgttatgttg-gtattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACGGTGCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 3
------gcatgtgtccattttctac-tatt-caaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
       |||| ||    | |  |  |||| | | || | |   |    ||    ||   ||| ||  |    || |     |  |||| |  ||   |||||||||||||||||||||||||||||||||  |||||||| || || |||||||| ||||| ||||||||||| |||||||||||||| |||||||| ||
acatatacatgagtgggatatacatgtatttccacattaattcctcacgaccagtattatttccttattttcttgtctttgttatgttg-gcattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACAGTTCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
   | |||  ||   |  || |    | | | ||||| || | | ||||   |   |   |||    |  ||  |          |    ||||||||||  | || |||||||||||||||| |||||| || ||||||||||| || |||||||| || ||||| || ||||| |||||||| ||||||||
--gtttgtatatcaccatctgtcttgattcattcttt-tataatcacattgttctttccctgaatcaattccttt----------taaaacagGTATTGTATTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
   | |||  |||  |  || |    | | | ||||| || | | |||||  |   |   |||    |  ||  |               ||||||||||| | || |||||||||||||||| |||||| || ||||||||||| || |||||||| || ||||| || ||||| |||||||| || |||||
--gtttgtatattaccatctgtcttgattcattcttt-tataatcacatcattctttccctgaatcaattccttt----------caaaacagGTATTGTGTTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
|  ||| |   | | |  || ||  || | |   |||      |  |||| | |  ||  |    |||  | | | | || ||       ||||||||||  | || ||||| |||||||| | |||||| |||||||||||||| || |||||||| |||||||| |||||||| |||||||||||||| ||
gtttgtatttgtatccatctgtttcaattcatagttt------tgtcatcacattgttctttccctgaatcaaatactttctgaa----acagGTATTGTTTTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
|  |||    |||| |  || |   || | | || || |    | ||||   |  ||   |||    |  |       || ||  |    ||||||||||  | || |||||||||||||||| |||||| |||||||||||||| || |||||||| |||||||| ||||| || |||||||||||||| ||
gtttgtacttatttccatctgtcttaattcactcctt-tgtcttcacattgttctatccttgaatcaaatct------ttttgaat----cagGTATTGTTTTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G18780.1 (Arabidopsis thaliana), 3'ss of exon 2
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
            ||  |||  || |   |   | | | || ||| |    || | |||  |||  ||| | | |    |  |   |||  ||||||||||||| |||||||||||||||||| ||||||| ||||||||||| || || |   | ||||||||||| || || ||  | || |||||||| ||
-----------gttagtacattttaggctt--tttgtttatactcattgatcattatt--tgaactgagctctgattatcttccattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGTTTCTCTCTTCCTCATGCCATCCTCCGTCTTGACCTTGCTGGACG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtg-cagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
      ||   || |  |||  | || ||     | ||     |   ||||  | | | || || |      |||   |      ||||  ||||||||||||| |||||||||||||||||| ||||||| ||||||||||| || || ||||| |||||||||||||| |||||  | |||||||| |||||
------gttagttcttaact-ctaaacatccaagtctgagttatattatcttcttacttgt-atttacttaaagtcgttctctttttgtaacagGTATTGTGCTCGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGGTATGCTCTTCCTCATGCTATCCTTCGTCTTGATCTTGCGGGTCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatat------gaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
   |  || |||| |  |       |||     |   ||    ||   | | || | || | || |      || | |||||   ||    || |  |||||||||| | || ||||||||||||||| ||||||| ||||| ||||| || || |   ||||||| |||||||| || ||  | || |||||||||||
--gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatg-attttctttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
gcatgtgtccattttctactattcaaaatgagtctttgtacacttacatctcttcattggtgatatgaccccagtgcgttgtggct----tgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
    ||    |||     || ||   | ||    |||   || ||     | |   ||| |  | |  ||  ||| |    | |||    ||   |||||||||||| ||||||||||||||||||| |||||| |||||||| |||||||| ||||||||||| |||||||| |||||  | || |||||||| ||
----gttcgtattaaaatctttttggattggaatttt---cattt-ttcttttctgttgttagtgtagcctgagttctaacttgctcctttgactagGTATTGTGCTGGATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG

upper sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 2
-----gcatgtgtccattttctactattcaaaatgagtctttgt-acacttacatctcttcattggtgatatg-accccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
      || |  |   ||    | ||||   ||        | | |   |   |||   |  || || ||||  ||   |||   |||  |  ||   |||||||||  | ||||||||||||||||| |  || |||||||||||||||||||||||||| ||||| ||||| || ||||| || || |||||||||||
aaatttcaagaattttttcctcagtattggtaactgccgactatgattttcttatcctgttctttgttatatttactgaagttttttggtgtgtgaaaagGTATTGTCTTGGATTCTGGTGATGGTGTCAGCCATACAGTGCCAATCTATGAAGGATATGCTCTTCCACATGCAATCCTTCGATTAGACCTTGCTGGTCG

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|58675857|gb|CK064544.1|CK064544
EST:     TGTGGCTATTCAAGCTGTTCTTTCACTATATGCCAGTGGTCGTACAACAG                         GTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATG
genomic: TGTGGCTATTCAAGCTGTTCTTTCACTATATGCCAGTGGTCGTACAACAGgcatgtgtcc ... gcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATG
EST: gi|29639531|gb|CB644540.1|CB644540
EST:     TGTGGCTATTCAAGCTGTTCTTTCACTATATGCCAGTGGTCGTACAACAG                         GTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATG
genomic: TGTGGCTATTCAAGCTGTTCTTTCACTATATGCCAGTGGTCGTACAACAGgcatgtgtcc ... gcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATG

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: 72 (upstream exon), 64 (downstream exon)
Score: 34

GAGAAAATGACCCAAATCATGTTTGAGACATTCAATGCACCAGCAATGTATGTGGCTATTCAAGCTGTTCTTTCACTATATGCCAGTGGTCGTACAACAGgcatgtgtcc ... gcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacacttacatctcttcattggtgatatgaccccagtgcgttgtggcttgtgcagGTATTGTGCTTGATTCTGGTGATGGTGTGACTCACACAGTGCCAATCTATGAAGGATATGCACTTCCTCATGCTATTCTTCGGTTGGATCTTGCTGGTCG
  cacttac  putative branch site (score: 34)