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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_Os07g47290.3
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|29637953|gb|CB642962.1|CB642962
EST:     GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG                         CTGCCACCATG
genomic: GAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAGgttagtttct ... aaatttgcagCTGCCACCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtcattcaaggtagcttacagtggcagtgtcataactccatggaaaatttgcagCTGCCACCATGAGCTTGAGACTGCAAGAATTAATGGTCTGCTTGGGAATATTGATGCCAACACTGGTGATCCCCAGATCG
                              tcataac  putative branch site (score: 2)
                                            aaaattt  TA-rich tract