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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcttgcttccctaacgtcattcaaggtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG

Basic information

species Oryza sativa
transcript LOC_Os07g47290.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G427620_T01 (Zea mays), 3'ss of exon 7
------------gttagttt--cttgcttccctaacgtcattcaaggtagcttacagtg-gcagtgtcataactc---------catggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
            | || | |  || |   |   || |   ||   | | |  || | || |  |  | ||| ||          ||||  ||| |||||||||||| |||||  | ||||||||| | |||||||| |||||||| ||||| ||||| |||||||||||||| ||  | |
gagtgcaaccatgctactctatctggacacaggaaaggtttttttgcttggctaaattgagttgaataatagcttaaagatttgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 14
gttagtttcttgcttccctaacgtcattcaaggtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
|| | ||| |||||| |||||| ||| |||    |  |   |  |          |||| ||||  ||| |||||||||||| ||||| || ||||||||| | |||||||| ||||||||||| |||||||| |||||||||||||| ||  | |
gtaatttttttgcttgcctaacttcagtcatataatttcttaaag----------aactacatgttaaacttgcagCTGCCATCATGAACTGGAGACTGCACGCATTAATGGGCTGCTTGGGAACATTGATGCAAACACTGGTGATCCTCAAGTTG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 14
gttag--tttcttgcttccctaacgtcattcaag--gtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
|| ||  ||| |||||| |||||  | | |  |    ||||||| ||            |||| ||||  ||| |||||||||||| |||||  | ||||||||| | |||||||| |||||||| ||||| ||||| |||||||||||||| ||  | |
gtaaggtttttttgcttgcctaaattgagttgaataatagcttaaag------------aactgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G544990_T01 (Zea mays), 3'ss of exon 12
-------------------------gttagtttcttgcttccctaacgtcattcaaggtagcttacagtggcagtgtcataactc-catggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
                         |  |  |    | ||   |  | |   | ||   || |   | |   ||  | |  | |  ||||  ||| |||||||||||| |||||  | ||||||||| | |||||||| |||||||| ||||| ||||| |||||||||||||| ||  | |
gagtgcaaccatgctactctatctggacacatgaaaggtttttttgcttggctaaattgagttg--aataatagcttaaagatttgcatgttaaacttgcagCTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------gttagtttcttgcttccctaacgtcattcaaggtagcttacagtggcagtg-tcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
                                                       | | |||  |  |     | | | | | ||  | |   ||  |    ||  | | || | |      |  | | || || || |||||||| || |||||||| || |||||  |||| || ||||||||||| |||||||||||||| ||  | |
gtgaatcgatcattgtatattgtgtttacatgggctgtccttgatctttcccttttaaatttgatattcataaatcataactgaaactggac-acgttctttgtacttacaatttctgttgtacctggtagTTGTCATCATGAGCTCGAAACTGCAAGGATCAATGGATTGCTGGGTAATATTGATGCAAACACTGGTGATCCTCAAGTTG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 15
------------------------------------------------gttagtttcttgcttccctaacgtcattcaaggt--agcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
                                                ||| ||  |||  |||   |   ||| | ||||   |   |||      |    | | |||   ||   |   |||||||| || ||||||||||||||||||||| | |||||| | || || ||||||||||| |||||||| || || || || |
gtttgtcctataattttgtttcaagcttttctaatgtcttgcctgcatgtttgtagctt-tttcttgataatcacttaaggataaaactacttctttatgaactttactatgtgtgtaccatgcagCTGTCATCATGAGCTTGAGACTGCAAGACTCAATGGTTTACTGGGAAATATTGATGCTAACACTGGCGACCCTCAAATTG

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|29667757|gb|CB664032.1|CB664032
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|29625367|gb|CB630378.1|CB630378
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|29643120|gb|CB648127.1|CB648127
EST:     GAGTTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|12622805|gb|AU173018.1|AU173018
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|29661148|gb|CB657423.1|CB657423
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|5004160|gb|AU069309.1|AU069309
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|29665147|gb|CB661422.1|CB661422
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|29637953|gb|CB642962.1|CB642962
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATG
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATG
EST: gi|29620969|gb|CB625980.1|CB625980
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
EST: gi|29644690|gb|CB649697.1|CB649697
EST:     TTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT
genomic: TTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATAT

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), 51 (downstream exon)
Score: 71

GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcattcaaggtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
                              tcataac  putative branch site (score: 71)
                                            aaaattt  TA-rich tract