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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt...

Basic information

species Oryza sativa
transcript LOC_Os09g21770.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G091265_T01 (Zea mays), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt--
          || ||||||||||| ||||||||||| || ||||||||||| || |||||||||||||||||||   ||  |  |  |||  || |||| | |      ||  ||     || |   || || |  || |  |    | | ||       | | |  |   
----------TGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttc-tcccattagtgcatgttttgagaggggtttat-ctagtaaaatcactgtgaaatggctccacattttgccc

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt--
 || |||||||| ||||||||||| ||||||||||| || ||||||||||| || |||||||||||||||||||   ||  |  |  |||  || |||| | |      ||  ||     || |   || || |  || |  |    | | ||       | | |  |   
ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttc-tcccattagtgcatgttttgagaggggtttat-ctagtaaaatcactgtgaaatggctccacattttgccc

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G091265_T03 (Zea mays), 5'ss of exon 2
-------------------------------GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt--
                                || |||||||| ||||||||||| ||||||||||| || ||||||||||| || |||||||||||||||||||   ||  |  |  |||  || |||| | |      ||  ||     || |   || || |  || |  |    | | ||       | | |  |   
TGATCTTATGTGACATTGTTTGTATGTGAAGATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttc-tcccattagtgcatgttttgagaggggtttat-ctagtaaaatcactgtgaaatggctccacattttgccc

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G20180.1 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtc-atttttaggaggaagtatcatagactcagt--
||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||||||   ||| || |  || ||    |    |  ||  |     ||   | ||  |   |  |||   |  |  | |  |   | ||||     | |      
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaag--actcggtg-tattctgctttactttgttgtgttattgtgtttggagtttggattttgcttatttaggtgtttgtttatgtatgtggaatttgagaa

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtc-atttttaggaggaagtatcatagactcagt---------
||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||||||  | |   ||   || || |  |     |||   | |||  |   | |   | ||| |||   ||  | ||| || |  |  | | ||  |||  ||         
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactc---ggtttattctgattt-----actttgtttgga-gtttggattttgttt-atgtatgtggaatttgagaaatagatgttatttactgggttgaagggat

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G35680.2 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttc-atgcccgtcatttttaggaggaagtatcatagactcagt--
||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||||||| |   ||    | | ||| | ||   |||||    |   |    ||  ||| |||  ||| |||    | |        || || | |  |   ||  
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaagccagtgtattc-tgctttctttgtttactgttattacatttgtgagtggtttttggatgtccg--ggtctctaattttagcattagatgcgttgttt

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt-
||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||||||| |   |     |  | ||   ||   |||||    |   |    ||  ||| |||  |   | |  || |        || || | |  |   || 
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaaaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtc-tggttctctaattttagcattagatgcgttgtt

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv12s0059g01180.t01 (Vitis vinifera), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttca-tactgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagta-tcatagactcagt
||| || |||||||||||||| ||||| ||||| || || |||||||||||||| ||||||||||||||||| |    |||   |  |  |     |||| |  |||      || | | || |  |||  ||||||   |  |||  ||||   |  |  || |    | 
GTATTGTAAGTGCGAGATGCCTTATAATCCGGACGACCTTATGGTGCAGTGCGAAGGATGCAAGGACTGgtatacttgttgcatattttttatttgttcagttatgcggaaaactaatcaaaagaaatta-atgccctgtacatttgtgaggttttggttttaaatattg-

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcacttggggacatccttacctttcatactgcatctggctgaccgaagggt-atttcatgcccgtcattt-ttaggaggaagtatcatagactcagt
||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||| |||||||||||||||    |||  |    || ||   |    | | |  | | | ||      | || ||||||     ||   |  ||  |   ||  ||   | |||||  
GTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTGgtaacctgcttttgttattcttttgttgggtttccggttgttgttgtgttttgtgtcatttcagttttgtatctgattttgtaaaaacat-ggaaactcaa-

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaa--atcacttggggacatccttacctttcata-ctgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt
||||||||||||||||||||| || |||||||||||||| ||||||||||| ||||  ||||| |||||||||  |||| ||     ||     |     | |  | || || |    |   || || |                                           
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag------------------------------------------

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|58598945|gb|CK009473.1|CK009473
EST:     CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCAGCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
genomic: CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
EST: gi|33663380|gb|CF294347.1|CF294347
EST:     CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCATCCATCTTGTATGGGAATGACCATTGAG
genomic: CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAG
EST: gi|86256715|gb|CI061478.1|CI061478
EST:     CCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
genomic: CCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
EST: gi|29638119|gb|CB643128.1|CB643128
EST:     CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
genomic: CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
EST: gi|29638253|gb|CB643262.1|CB643262
EST:     CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
genomic: CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
EST: gi|33658502|gb|CF281115.1|CF281115
EST:     CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
genomic: CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
EST: gi|29638118|gb|CB643127.1|CB643127
EST:     CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG                         GTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA
genomic: CCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGA

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: 69 (upstream exon), 69 (downstream exon)
Score: 42

GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaaatcact ... acttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGATCATTTCCTGTGCGCAGATTGTGTCAAAGAAAATGGCACGAAGAGACCT




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