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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG

Basic information

species Oryza sativa
transcript LOC_Os04g51610.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
----------------------------------------------------------gtttatctctcgact---aatgttccatcatgtt-ttgaaagaaacaatcttc-----atgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
                                                           ||||    |  |||   ||  | | |  ||||  || | | || ||   |||     |||||||| || |||  | | ||  |  |||   ||  |||||  |   |||||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
--------------------------------------------------------gtttatctctcgactaatgttccatcatgtt-ttgaaagaaacaatcttc-----atgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
                                                        |   ||       ||| | | | |  ||||  || ||| || ||   |||     |||||||| || |||  |    |  | |||  | ||  |||||  |   |||||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagt-tcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G138195_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------gtttatctctcgacta---atgttccatcatgtt-ttgaaagaaacaatcttc-----atgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
                                                    ||||     |  |||    |  | | |  ||||  || ||| || ||   |||     |||||||| || |||  |    |  | ||     ||  |||||  |   || ||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcatcggtttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtactcgacaaactctgaaacttgcagACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
--------gtttatctctc-gactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
         | |||   || |||  |  ||   |  || ||  ||  |   || ||  |  ||       |||  |   || ||| | |  | ||  |  | ||  ||||| ||||| |||||  | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |
ctattagaatctattgttcagacacacatt---ttttggttcaaattaggtaaact--agtttttgttttcatggtt--gtttttgtgactctatttttgagtt--tagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 27
gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaat---agGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
  ||   | ||        |||  | || ||   ||| ||    | || |     || | || |  |  |||   |||| |||  | ||    |  ||   |||||||||| ||||| || |||||||||   |||||||||||||| || || || || |||||||| ||| | || ||||| |||||||| || || | |
-attggttgtcatgctccattctctaatatt--aaaataattcctgtttactaaaaagatccttgttatagttaatcttgtgctttactattttgtattttagGCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaat---agGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
    |||| |    |  |  |    ||| | || ||| ||    | || |     || || | |  |  |||   |||  |||  | ||    | |||   |||| ||||| ||||| || ||||||||||| |||||||||||||| || || || || |||||||| ||| | || || || |||||||| || || | |
---catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
gtttatctctcgactaatgttccatcatgtttt--gaaagaaacaatct---tcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
 | ||| |     ||| |||||   ||  ||||  |    |||  || |     |  ||       |||  |   || | |    |  | |  || | ||  ||||| ||||| |||||  | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |
-tctat-tagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgac-tctatttttggagtt--tagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 24
gtttatctctcgactaatgttccatc----atgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
 |  |  | |  ||||   |||||      |||||||      ||     |  |    |    |   |  ||  ||  |||| || || |  || | |  |||||| |||||||||||  | ||||| ||||| || || ||||||||||| ||||| || ||||| || || ||||||||||||||||| || || |||| |
-taaaggtttgaactatcattccaatgcagatgtttttgttctaatgcagtaaactagcttttattcttttcttgtaattct-atacatttttggaat--atagGCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 26
---gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatg-ttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
   ||| |  | |  | |  |  |   | |    | ||    | ||||  |  |  ||     |  ||| |  |  |  |  | | | ||  || | ||  ||||||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||| || || | |
aaagttgaaatttaaaat--tcattattaaaacctagagtttatcaattatattaatttccttattatagttgatacagtgctttactattatgtaatt--tagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 24
gtttatctctcgactaatgttccatcat----gttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgc----tgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
    |  | |  ||||   || ||        |||||      ||        |   | |  | |  | || | || ||| | || | || |    || | |  |||||| |||||||||||  | ||||| ||||| || || ||||||||||| ||||| |||||||| || || ||||||||||||||||| || || |||| |
----aggtttgaactatcatttcaatgcaggagtttttgttctaatg--tagtaaactaactagcttttattctgtttttgtaattctatacattttggaat--atagGCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 26
----gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
        |   |   |||     |  |    | |   ||| |   ||| ||    ||     |  ||| |  |  |  | || | | ||  || | ||  ||||||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||| || || | |
gggtaccaaatccgaaactggaaataaactgggatc--aaaaatgtaattttaccatttttttattatagtttatacaatgttttactattatgtaatt--tagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 26
---------------------------------------gtttatctctcgactaatgttccatcatgttttgaaagaaaca-atcttcatgttcaacaaccataatccagtctttcttatgcaa----tgctgaacttaat---agGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
                                          ||  |||     || ||| | |   |    | |     |  |  ||  |  ||| | | |  |      |||   |  ||  |    |  |||   || |   |||||||||| |||||  | ||||| ||    ||||| ||||| || ||||||||||| || || ||||||||||||||||| ||||| || || || | |
gtatagtaatttactgaaatttaaactgataatgtcgaaagctacatctaactgaaagtttcttttggccaagtattttgcctacgtttttactcagcgagcggatcattatctcattggtgttaaattttttgagtgtatttgcagGCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 24
gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
         |   ||||   | |  || ||| || |  |        |  |||   |   ||| ||||   | |||||| ||      || |||  ||||||||||||||||||||| ||||| ||    |||||||||||||| || ||||||||||| || || || ||||||||||||||||| || || || | |
--------gttctctaacaattctacaggttatgtattatgtg----ttgtgtgtcatctcca-aatctgatttttcttttgttgctttggact--atagGCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
||| |   |   | | |  |||| || | | |  ||      ||  | ||   | |   |  || |  |  ||| | ||   |    |  |||||   ||||||||||||||||| | ||||| ||||| || || |||||||| ||||| |  || || || || |||||||||||||| |||| ||| || |||| |
gttcaatac---atttacattcc-tcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccc----cccaacttt-cagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
gtttatctctcgactaatgttccatcatgttttgaa--agaaacaatcttc---atgttcaacaaccataatc-----cagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
        ||| | ||   ||| |  || ||||  |  | ||||| | ||    || |||  |   | |  ||        | |||||| |    |  || ||||  ||||||||||| |||||  | ||||||||    ||||| || ||||| || ||||| ||||| || || |||||||||||||||||||| || || || | |
--------ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggactt--tagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 26
------gtttatctctcgactaatgttccatcatgttttgaaagaa-acaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
       | ||    | |  |  ||||    ||| ||  | | |   | ||| ||  |  |    ||  ||    |||  | | | ||    |  ||       |||||||||||||||||||| |||||||| || |||||||||||||| || || || || || || || ||||||||||| || ||||| || || || | |
ttatggctgtagagtttggatgttgtttttccatcttcagcaggttcataatgttgtttctttgtaatgattgatcaggttgtatcattttctattg-------tagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG

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|58594188|gb|CF992496.1|CF992496
EST:     GGCACAAATGATGCCCCAGCTTTGCATGAG                         GCAGATATAGGTCTCTCCATGGGCATCGAGGGAACTGAAGTTGCCAAGGAG
genomic: GGCACAAATGATGCCCCAGCTTTGCATGAGgtttatctct ... aacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAG




















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: 67 (upstream exon), 68 (downstream exon)
Score: 24

ACCAAATGACAAGCTTTTACTTGTTAAAGCATTAAGAAAAAGAGGTCATGTTGTTGCTGTGACTGGAGATGGCACAAATGATGCCCCAGCTTTGCATGAGgtttatctct ... aacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG
                                             aacttaata  TA-rich tract