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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG

Basic information

species Oryza sativa
transcript LOC_Os03g63710.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G176612_T01 (Zea mays), 3'ss of exon 1
gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtactag----tattgtcgtgtgcttgttaatttcc--cagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                     | | | ||   || |   |||       |  |  ||| ||  |       || ||||     | |      | ||  ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| |
----------------gtgcgtgcgtattgccctgcgctgccatggatctagggcctcctgctccgccggctactgtctctcacatcacgtctccctgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 1
gtaacttcctcctctcagatcttcttcttcttcttcttcgcctcaagagtcagatctcatgtacta--gtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
              |  |  ||| ||   || | |    |||    ||   ||  ||| ||       | ||  ||   |      |    |  ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || |
-------------gtacgtgcttattggcctgcctgcctgccctg-gatctaggcctcctgcttcgccggatcctcagatcacatctctccttgcagATGTGCTTCGACTGCAACGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------------------------------------gtaacttcctcctctc-agatcttcttcttcttcttcttcgcct-----caagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                                                                              ||   |||    |  | ||||||  ||     ||| |    |||        | ||  ||| |  || | | |||| ||  | |  |||||  |||  |||||||| ||||| ||||  || |||||||| |||||||| |||||||| || || ||||| |||||| |||| ||||||||||| |||||||| |||||||
gtttggtttttgtaattttgaatttcgaatttcaatttgagtgcataatcgttggttccgtgatttcgttttatacagtttgaaattttcgtttgtggtttctgatttacgagatctggtttcagatctgcaatacctgtgcttgtgcgtttgatttt-tgaattggtatggtttttttgttgtttttttttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------------------gtaacttcctcctctc-agatcttcttcttcttcttcttcgcc-----tcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                                                                       ||   |||    |  | ||||||  ||     |||      ||     |   | ||  ||| |  || | | |||| |   | |  || ||    |  |||||||| ||||| ||||  || |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||| |||||||| |||||||
gttttttgtttataattttgaatttcaatttgagtgcataatcgttggttccgtgatttcgtttaatatagtctgaacttttcgtttgtggtttctgatttacgagatctggtttcagatctgtgatacccgtggtagtgtgtttgatttt-tgaatttgtatggcttttttttttttttaatttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCG

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------gtaact-tcctcctctcagatcttcttcttct----tcttcttcgcctcaagag---tca-gatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                                 ||   | |  |  | |  | | ||||  |  |    |||  |||   ||  |||   ||  |||   || |     | || |  |||   | ||   ||   ||||||| || || || |  || |||||||| || ||||| |||||||| || || |||||||||||| |||||||||||||||| ||  | || || || |
gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgtttttattttggtttttggttttctgttcttgagatctggttcagatctggaggtttcgcgattggatctcggttttttattttgtttctttttggtttttagATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGG

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|88739668|gb|CI763176.1|CI763176
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88364273|gb|CI612222.1|CI612222
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGGAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88302091|gb|CI667937.1|CI667937
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88826434|gb|CI776999.1|CI776999
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88361014|gb|CI604581.1|CI604581
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|428827|gb|D24983.1|D24983
EST:     CCGACAAGAACGCCGTNTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58658150|gb|CK046830.1|CK046830
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCCAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58664331|gb|CK053017.1|CK053017
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|66916299|gb|CX103147.1|CX103147
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88721612|gb|CI744911.1|CI744911
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88341494|gb|CI635692.1|CI635692
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29645173|gb|CB650180.1|CB650180
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58680319|gb|CK069006.1|CK069006
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|58677850|gb|CK066537.1|CK066537
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|87006728|gb|CI285762.1|CI285762
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCCAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29677839|gb|CB674114.1|CB674114
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29635513|gb|CB640522.1|CB640522
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88288415|gb|CI661620.1|CI661620
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88723709|gb|CI747219.1|CI747219
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|88351379|gb|CI627395.1|CI627395
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAT                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|11443001|gb|BF430888.1|BF430888
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|29679055|gb|CB675330.1|CB675330
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
EST: gi|33654274|gb|CF276888.1|CF276888
EST:     CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAG                         ATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC
genomic: CCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTAC

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: 75 (upstream exon), 75 (downstream exon)
Score: 58

GGCTGCCTGCCTGACAAGAGAGGCAGCAGCCATGGCGTTCGACGCCTTCACCGACAAGAACGCCGTCTTCCGCCGCCTCAAGGCCAAGCCCGAGAACAAGgtaacttcct ... aatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcaagagtcagatctcatgtactagtattgtcgtgtgcttgttaatttcccagATGTGCTTCGACTGCAGCGCCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCG
                                         tgttaat  putative branch site (score: 58)
                                               tttccc  CT-rich tract
                                        ttgttaattt  TA-rich tract