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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcacaagtttccttactttgtgcattgctcaagattttcaccatctgaactgttttgacataactgtttggtgaacataatttcgtttggtgttt...

Basic information

species Oryza sativa
transcript LOC_Os06g45710.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G41550.1 (Glycine max), 5'ss of exon 4
TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcacaagtttccttactttgtgcattgctcaagattttcaccatctgaactgttttgacataactgtttggtg-aacataatttcgtttggtgttt
||| |||||||| |||||||| || ||||||||||||||||| ||||| |||||| | || || ||||  || |||||||| || ||||| ||||||||||| ||| |  |  |   ||  |   | ||||    |  || ||    |  |      |||  | | |  || ||| |   |  || |||   ||| |    
TGTGAATGATGCATTTGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgt-ttgtaggaagtaa-ttgttagcttcattatatat-atattgggtaattatgtaattt--atacagttgattgatctgatgtatttttaattgtttcag

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcacaagtttccttact-ttgtgcattgctcaagattttcaccatctgaactgttttgacataactgtttggtgaac-ataatttcgtttggtgttt---
 || |||||||| || ||||| || ||||||||||||||||| ||||| |||||  | || || ||||  || |||||||| || ||||| ||||||||||| ||| |  |  |         ||||    | |   | ||          | |  | | |        | ||||  | | |  | ||||  ||   |||||   
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgt-ttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcacaagtttccttactttgtgcattgctcaagattttcaccatctgaactgttttgacataactgtttggtgaacataatttcgtttggtgttt
 || ||||||||||| || || || ||||||||||||||||| || ||||||||| | || |  ||||  ||||| |||||||||||||||||||||||||||||  | || || |   |    | | ||      ||||    |   |||  | | |  |||    ||| ||   ||    | |||  ||  |      
CGTTAATGATGCCTTCGGAACTGCTCACAGAGCTCATGCTTCCACTGAGGGAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatt-taaaatttgcagcataaagagtatcttcttagat---gagtctctttattttactgatcagactattacttg--ttttattgtgtcag------

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 5'ss of exon 3
TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcacaagtttccttactttgtgcattgctcaagattttcaccatctgaact-gttttgacataactgtttggtgaacataatttcgtttggtgttt--
||| |||||||| ||||| || || |||||||| ||||| || |||||||||||| | || || |||| |||||| |||||||| ||||||||||||||||||| |      |  | ||    |     || ||    ||   | |||    ||   ||| | |  |    ||    |  | | |  |   ||  |   ||  
TGTGAATGATGCATTTGGAACCGCTCACAGAGCCCATGCATCTACAGAGGGAGTTGCTAAATACTTGAAACCTTCGGTTGCTGGCTTCCTCATGCAGAAGgtatggtggtgatcactttttaatacatcttcctttccatgccctccaataaaataagttctaatct---cgtagaatccatacatgtatattaagctcttgg

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|218487293|gb|FG966815.1|FG966815
EST:     TTCCTCAT-CAGAAG                         GAACTTGACTATCTTGTTGGAGCTG-TGCCAACCCCAAAAAACCATTTGCT
genomic: TTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|218492325|gb|FG948433.1|FG948433
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|29675440|gb|CB671715.1|CB671715
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|33677818|gb|CF306057.1|CF306057
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCT
EST: gi|58689757|gb|CK078444.1|CK078444
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAANCCCAAAAAACCATTTGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|218487061|gb|FG967311.1|FG967311
EST:     AGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
genomic: AGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|33822979|gb|CF337294.1|CF337294
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTGGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|33807809|gb|CF329796.1|CF329796
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|33693456|gb|CF321695.1|CF321695
EST:     GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
genomic: GAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT
EST: gi|218480492|gb|FG970510.1|FG970510
EST:     GAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAG                         GAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCATAAAACCATTTGCT
genomic: GAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCT

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: 70 (upstream exon), 75 (downstream exon)
Score: 88

TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcaca ... accaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCTGCCATTGTTGGTGGATCCAAGGTGTCAACAAAGATTGGGGTGATTGAGA




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