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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaaactatagtactctcctttaatctacaaaattaaatttcaagggttgatctttcttttgtcatattgtctttcatggtcag

Basic information

species Oryza sativa
transcript LOC_Os08g31030.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g31030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G02790.1 (Glycine max), 5'ss of exon 5
ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaaactatagtactctcctttaatctacaaaattaaatt-tcaagggttgatctttcttttgtcatattgtctttcatggtcag---
|    ||  |||||||     | || |||||| | ||||| || || || | |  |||||||||||||||||| ||||| || || |||||||||||||||||    || | | | |  |||  |||        ||||    | | |  || | |     | |   |   |      ||  |      ||    |    
ATAAGGTTCTTGGTGTTGATAGACTCCGTGTGGTTGATGGCTCAACATTTTCTGAGTCACCAGGAACCAACCCTCAAGCTACTGTGATGATGATGGGCAGgtatgtacatatatagaacataacactgagtaaacatctttggattaactttgttaccaacttactatatatagaagttagggcgccaaattactaataa

upper sequence: LOC_Os08g31030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G42630.1 (Glycine max), 5'ss of exon 5
ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaaactatagtactctcctttaatctacaaaattaaatttcaagggttgatctttcttttgtca--tattgtctttca---tggtcag-
|    ||  |||||||     | ||||||||| | ||||| || || || | |  ||| |||||||||||||| |||||||| || |||||||||||||||||    || | | ||  || |  |||        ||||     ||| | |||      ||  | ||  |     ||  | ||   | | |   | || || 
ATAAGGTTCTTGGTGTTGATAGACTTCGTGTGGTTGATGGCTCAACATTTTCTGAGTCGCCAGGAACCAACCCTCAAGCCACTGTGATGATGATGGGCAGgtatgtacatagagaacata-aacactgagtaaacatct-ttggattgacttttttttattattattattaccagcaaatgttaattatgagttttgttagt

upper sequence: LOC_Os08g31030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G72970.2 (Arabidopsis thaliana), 5'ss of exon 6
ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaa-actatagtactctcctttaatctacaaaattaaatttcaagggttgatctttcttttgtcatattgtctttcatggtcag
 |   ||  ||||||||    | ||  | || || ||||| || || ||      ||| |||||||||||||||||||| ||  | ||||||||||| |||||||  ||||| ||  || |   || |        |  |  |   ||   ||| |  | |  || | |     |     |||||  || | | |||
GCAAAGTTCTTGGTGTCGACAGGCTCAGAGTTATTGATGGTTCAACGTTTGACGAGTCTCCAGGAACCAACCCGCAAGCTACTATGATGATGATGGGAAGgtaaat-caaaatcattaccaacataat-------gaattggaggttttcttttta--gttcaatatataaacagaggatttgtcaatctttg-cag

upper sequence: LOC_Os08g31030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g02210.t01 (Vitis vinifera), 5'ss of exon 5
ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaaactatagtactctcctttaatctacaaaattaaatttcaagggt--tgatctttcttttgtcatattgtctttcatggtcag
|    ||  |||||||     | || || || || ||||| || || ||      ||||||||| || || || ||||| || |||||||||||||||||||||   ||      | |||||    |     | |||  ||   |   |  ||||| |    ||   |||||||||      ||| |           
ATAAGGTTCTTGGTGTGCACAGGCTCCGAGTAATTGATGGTTCAACGTTTAGGGAGTCACCAGGCACTAATCCTCAAGCGACTGTCATGATGATGGGCAGgtaagatca----ttacctatatgtttagaaataaatgaacccgaaccatcttcaaagaaaatgtaatttcttttggtgatatgtgtgcag-------

upper sequence: LOC_Os08g31030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ07664 (Selaginella moellendorffii), 5'ss of exon 3
ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaaactatagtactctcc--tttaatctacaaaattaaatttcaagggttgatctttcttttgtcatattgtctttcatggtcag
     || || |||||      ||| || ||  | ||||| ||||| ||  |    || |||||||||||||||||||| || |||||||||||||| ||| ||  | ||   |    |  |||    |||   | |||||  |  |     | |  ||                                       
----GGTCATCGGTGTGAATAACCTCCGAGTCGTAGATGGATCGACGTTTCTGTCATCTCCAGGAACCAACCCGCAAGCTACTGTCATGATGATGGGAAGGCAA-

upper sequence: LOC_Os08g31030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ07720 (Selaginella moellendorffii), 5'ss of exon 3
ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaaaaacaaactatagtactctcctttaatctacaaaattaaatttcaagggttgatctttcttttgtcatattgtctttcatggtcag
     || || |||||      ||| || || || ||||| ||||| ||  |    || |||||||||||||||||||| || |||||||||||||| ||| ||          || ||      | ||       |  |    | | ||| || ||   |||    |||   |                      
----GGTCATCGGTGTGAATAACCTCCGAGTCATAGATGGATCGACGTTTCTGTCATCTCCAGGAACCAACCCGCAAGCTACTGTCATGATGATGGGAAGGCAAg--------taagct------ccctttccagttgcatcggactgaatctctag---tgactcgtctgcag----------------------

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|86886682|gb|CI334596.1|CI334596
EST:     TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAGGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|86841933|gb|CI338345.1|CI338345
EST:     TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|88282919|gb|CI402119.1|CI402119
EST:     TTTAGGTCACCAGGAACCAACCCCCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|86881989|gb|CI324197.1|CI324197
EST:     TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|88279821|gb|CI401019.1|CI401019
EST:     TTTAGGTCACCAGGAACCAACCCCCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGGTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|86871401|gb|CI329798.1|CI329798
EST:     TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|88279720|gb|CI400918.1|CI400918
EST:     TTTAGGTCACCAGGAACCAACCCCCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|89196412|gb|CI398998.1|CI398998
EST:     TTTAGGTCACCAGGAACCAACCCCCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|86877444|gb|CI312789.1|CI312789
EST:     TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
EST: gi|86863590|gb|CI345272.1|CI345272
EST:     TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAG                         ATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT
genomic: TTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGT

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: 40 (upstream exon), 45 (downstream exon)
Score: 3

ACCGTGTGATTGGTGTCTCAGGCCTTCGTGTGATCGATGGGTCGACCTTATTTAGGTCACCAGGAACCAACCCGCAAGCCACAGTCATGATGATGGGCAGgtaaaggcaa ... tcatggtcagATACATGGGAGTGAAGATTCTAAGAAGAAGATTAGGACGAGCTGCTGGAGTATAACTGATTCTTGGACCTTATTGATTATGTAAGAATGTGACTTAGGAA




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