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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag

Basic information

species Oryza sativa
transcript LOC_Os07g01030.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G100652_T03 (Zea mays), 5'ss of exon 6
CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgta--tgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag
||||||| |||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||    ||||||||| |||||||||||||  || |   ||||||   ||    |||  ||||| | |      |      |||         ||||  || ||| | ||   ||   | ||| |                                                                    
CCAATAAAATACGCCTTTGGAACAAGGGTGTTGACTCAGAAAGCTTCCATCCTCGTTTCCGCAACATGGAAATGCGTTCAAGGCTAACgtacatgcatattcctcttcccttttgtgcagttttgta-tttgtccgtttcaatgcccgggccgaactg--tggtgc-taatgttttcgttggagcag-------------------------------------------------------------------

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA03G14200.1 (Glycine max), 5'ss of exon 8
CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgcta-aattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag
| || |||||  | ||||||||||||||||| ||||| ||||| |||||||| || |||       | ||||||||   |||||| | ||    |   |   |  |  |||  ||||         |  | ||  ||||| | |  ||||  | ||   | |||  |||| ||                                                                                
CGAACAAGATTTGTCTTTGGAACAAGGGTGTCGATTCTGAAAGTTTCCATCCACGATTCAAGTCCCATGAAATGCGATTAAGGCTGAGgtgcagaccatttgccattttcatgtgccca---aggtttgatatttaatggggtttcaatttattcttaatcttgtgtcatacag-------------------------------------------------------------------------------

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G17680.1 (Glycine max), 5'ss of exon 7
CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag
| || ||||| || ||||||||||||||||||||||| ||||  |||||||||   | |||     | ||||||||   ||| |||| |||||  | ||  |||    |   |    |  |   |||   | |  |||  ||  | ||| |  ||  || ||    ||||  | ||  ||                                                                        
CTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAGgtatg-gaccttttct-cattttttcatatgctca-agttttggt--aataatg--acatttcatcttattcttaaa-catttgtcatacag------------------------------------------------------------------------

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G27840.1 (Glycine max), 5'ss of exon 8
CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag
| || |||||  | ||||||||||||||||||||||| ||||| |||||||| || |||       | ||||||||   ||| || | ||    |   |  ||  |  |||  ||||      || |   | |  |  |||  | || |  | ||   | |||  ||||  |                                                                                
CGAACAAGATTTGTCTTTGGAACAAGGGTGTTGATTCTGAAAGTTTCCATCCGCGATTCAAGTCCCATGAAATGCGATTAAGACTGAGgtgcagaccattttccattttcatgtgcc------caatgatgtttaatgggttttcaacttattcttaatcttgtgtcatatag-------------------------------------------------------------------------------

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA18G42540.1 (Glycine max), 5'ss of exon 8
CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaattgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag
| || ||||| || ||||||||||||||||||||||| ||||  |||||||||   | |||     | ||||||||   ||| |||| || ||  | ||  |||    |  ||    |  |   |||   |  |||||  ||  |  |    |   ||| ||    ||||  | ||  ||                                                                        
CTAACAAGATTCGTCTTTGGAACAAGGGTGTTGATTCTGAAAAATTCCATCCCAAATACCGCTCCCATGAAATGCGATTAAGACTAAGgtgtg-gaccttttct-cattttgtcatataatca-agttttg--gcaataatgtcatttcatcat--gttcttaaa-catttgtcatacag------------------------------------------------------------------------

upper sequence: LOC_Os07g01030.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G01220.1 (Arabidopsis thaliana), 5'ss of exon 8
CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatctcctctgtgctcagttgcctttttgcagtacagatgcaatggtgctaaat-tgctactggttgttgcctcattcattatgtagagaatattttgaaatgagcaattatattccctgtctaacagcatgcttatactttcccttttcctctatcag
| ||| |  | || |||||||| |||||||| ||||||||||||||| ||||||||||||||  | | |||||||||  ||| || | | | | |||    | |  | |   ||   | | |||| || | |  ||||| | ||      |||| |  ||| ||  | ||  ||| ||||   || |                                                                  
CTAATCAACTTCGACTTTGGAATAAGGGTGTCGATTCAGAAAGCTTCAATCCCCGTTTCCGTTCTCAAGAAATGCGTATAAGACTGAGgcaag-aatagaatatacgtttcttt---tatatgcattaaaaa--caatgatactttccacgctaatc-ttgatgtttaat--attttgtaattaacag-----------------------------------------------------------------

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|29613028|gb|CB618041.1|CB618041
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
EST: gi|29613025|gb|CB618038.1|CB618038
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
EST: gi|29657825|gb|CB654100.1|CB654100
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
EST: gi|157651839|gb|EX451473.1|EX451473
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCACTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
EST: gi|29667657|gb|CB663932.1|CB663932
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
EST: gi|29669005|gb|CB665280.1|CB665280
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
EST: gi|86848294|gb|CI292130.1|CI292130
EST:     GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAAC                         TAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT
genomic: GAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGT

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: 74 (upstream exon), 75 (downstream exon)
Score: 33

CCAATAAGATACGCCTTTGGAACAAGGGTGTTGATTCAGAAAGCTTCCATCCCCGTTTCCGTAATGACGAAATGCGTGCAAGGCTAACgtatgtaatc ... cctctatcagTAACGGTGAACCAGAAAAACCGCTTATACTGTATGTTGGTCGTTTGGGAGTTGAGAAAAGCTTAGACTTTCTTAAGAG




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