Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttccctatgatatagctgtgcacggcatgctgatcttttaatcttggcactcacctcattacctctcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g53110.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G159295_T02 (Zea mays), 5'ss of exon 8
CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttccctat---gatata-gctgtgcacggcatgctgatcttttaatcttggcactcacctca---ttacctctcgtgcag-----
 ||||||||||||| |||||||| ||||||||||| |||||||||||||  || | | ||   |||  |  |||         |   || | || | | |    |  ||  |     || | |||   |||      
TTGAGAGAGTACATCGATGACACGGAAGATTACATCAATATCCAGgtaatgttgcgccatatagatgcatactgccttttatttttcgaccattcagtttctaaatacattttggtttttcttctttcgcaatgcag

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G35260.1 (Glycine max), 5'ss of exon 8
CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaac---------atttccctatgatatagctgtgcacggcatgctgatcttttaatcttggcactcacctcattacctctcgtgcag
||| |||||||||||||||| || |||||||| |||||||| || ||||          |||| |  || ||||| |  |      |  |   ||    | |  ||       |  |  || | | |  |||||
CTGCGAGAGTACATTGATGATACTGAAGATTATATTAATATTCAAgtaagtagctagcaatttactgataatatatcaattggtatctggtgaatgacatgaaattcaagtgaagttttttccatat--tgcag

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G32350.1 (Glycine max), 5'ss of exon 8
CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaac---------atttccctatgatatagctgtgcacggcatgctgatcttttaatcttggcactcacctcattacctctcgtgcag
||| |||||||||||||||| || |||||||| |||||||| || ||||          |||| |  || ||||| || |      |  |   ||    | |  ||       |  |  || | | |  |||||
CTGCGAGAGTACATTGATGATACCGAAGATTATATTAATATTCAAgtaagtagctagcaatttactgataatatatctattggtatctggtgaatgacatgaaatttaagtgaagtttttttcattt--tgcag

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 5'ss of exon 9
CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaac--atttccctatgatatagctgtgcacggcatgctgatcttttaatcttggcactcacctcattacct----ctcgtgcag--------------
||  | ||||| |||||||||||||| || |||||||| ||||||||| |  |   |   |    | |  | |  ||    |  |||  | | ||| |  |   | |  | |  | ||    ||||| | |              
CTACGTGAGTATATTGATGACACAGAGGACTACATTAACATCCAGgtatccaaaaacgaaacctcaaaatttttaacatgttcttgaaatctgaatataagtcattatattaaaagctaaaactcgt-cggttttctattcacag

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 5'ss of exon 8
CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaac--atttccctatgatatagctgtgcacggcatgctgatcttttaatcttggcactcacc-tcattacctctcgt--gcag
||  | ||||| |||||||||||||| ||||||||||| |||||||||||  |       | |  | |  |    |     ||   |  | | | |  |   ||   |  | || ||   |  |  ||||
CTACGCGAGTATATTGATGACACAGAGGATTACATTAACATCCAGgtaaccaaaaatgaaaagtcagaatttcttaaatgttgtgaaaatgtaatttctcttacaggctataatcactgtttatttgcag

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv07s0141g00590.t01 (Vitis vinifera), 5'ss of exon 8
CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttccctatgatatag--ctgtgcacggcatgctgatct---tttaatcttggcactcacctcattacctctcgtgcag----------------------------------------------------------------------------------------
||| | || |||||||||||||| ||||| ||||||||||| ||||||| ||      |  |  | |  ||   |||   |  | ||  |   ||   |  |   | | |     |    |  | || |                                                                                         
CTGCGTGAATACATTGATGACACTGAAGACTACATTAATATTCAGgtaa-atggttggacaacttggtacttgacaccaaaaacagaattaaattggttgataatattgatggagtctttttacatgtattagacaaaaaggaaaatttctctcttactttaagaagtatttaaagataatattattgttttgtgatctagtgtgttccttgttgcag

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|86491085|gb|CI133718.1|CI133718
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|3763402|gb|AU030154.1|AU030154
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88845073|gb|CI083998.1|CI083998
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|38468461|gb|CF952592.1|CF952592
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|89181743|gb|CI113249.1|CI113249
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAAGTGTGCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAA-T-T-CAG
EST: gi|88456911|gb|CI529112.1|CI529112
EST:     ACGCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: ACGCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|86495286|gb|CI137919.1|CI137919
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|86496775|gb|CI139408.1|CI139408
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|27547079|gb|CA767318.2|CA767318
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88429897|gb|CI562708.1|CI562708
EST:     CAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88413290|gb|CI523851.1|CI523851
EST:     ATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: ATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88840990|gb|CI000952.1|CI000952
EST:     CTGAGAGAGTACATTGATGA-ACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88476382|gb|CI413653.1|CI413653
EST:     NTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|86874289|gb|CI335901.1|CI335901
EST:     CGCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CGCTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|313083966|gb|HO213749.1|HO213749
EST:     CATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|89178025|gb|CI391204.1|CI391204
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|86252029|gb|CI055766.1|CI055766
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|58674510|gb|CK063197.1|CK063197
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88963590|gb|CI029384.1|CI029384
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88442581|gb|CI544148.1|CI544148
EST:     TTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: TTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|58683065|gb|CK071752.1|CK071752
EST:     CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG
EST: gi|88448280|gb|CI555135.1|CI555135
EST:     AGAGTACATTGATGACACAGAAGATTACATTAATATCCAG                         CTTGACAACCACCGTAATCAGTTAATTCAG
genomic: AGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG

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: 66 (upstream exon), 62 (downstream exon)
Score: 51

CTGAGAGAGTACATTGATGACACAGAAGATTACATTAATATCCAGgtaacatttc ... tctcgtgcagCTTGACAACCACCGTAATCAGTTAATTCAG




<











<


<