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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG

Basic information

species Oryza sativa
transcript LOC_Os05g46360.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
------------------------------------gtaattgataattcca------atatatgtgagatggactga---cgatctgaaatgttcagtaccttctttctaacatca-tctatcacactagta----attgataattca--------aatgtaact-tggttattga--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                     |||||| | ||| ||      ||| ||||||     ||| |    | ||| || ||| | | |  || ||| ||   |   | | |   | |  |     |||||| ||  |        | | | ||| |  |||||          || | || ||| || |||||||| ||||| |||||||| ||||||||||| |||  |||||||||||| ||| | || ||                              
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG-----------------------------

upper sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
--------------------------------------gtaattgataattcca-----atatatgtgagatggactga---cgatctgaaatgttcagtaccttctttctaa-catcatctatcacactagta----attgataattca--------aatgtaact-tggttattga--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                       |||||||| ||| ||     ||| ||||||     ||| |    | ||| || ||| | | |  || |||  |  |||  | | |   | |  |     |||||| ||  |        | | | ||| | ||||||          || | || ||| || |||||||| |||||||||||||| ||||||||||| |||  |||||||||||| ||| | || ||                              
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG-----------------------------

upper sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------gtaat-tgataattccaatatatgtgag-----atggactgacgatctgaaatgttca-gtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaa---cttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                                           | |  || ||||   | || |  ||       ||  |||||  || |   || || | |||| |  || ||   ||  | ||| | | ||||| ||  || |||     ||    ||   | |||   || ||  ||| || |||||||| ||||| |||||||| ||||||||||| |||   ||||||||||||||| | || ||                              
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactga-aatttactattttgatgtacttgattgctg-tattgtgtat-ataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG-----------------------------

upper sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttca-gtaccttctttcta-acatcatctatcacactagtaattgataatt-caaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                                                || | || |  |    || |   |   ||  |||||  || |   || || | ||||    || ||  |   ||| ||| | |  | | | |  |  || |  ||      |     ||  || | || ||| || |||||||| ||||| |||||||| ||||||||||| |||   ||||||||||||||| | || |                               
gtagttaccacaagagctttcaaatagttttaaaaataattgatgattgtttgtcttatgacatgttaatgttgctaaagatgttctttttatatactga-aatttactattttgatgtactggattgctgtattgcatgtataatagcaattactatttctttcttataccctctctcatttccttataattagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACAG-----------------------------

upper sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatc-tatcacactagtaa--ttgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                                 | || |    ||||  |||   ||| || |  | |  |||  |||| | ||    | | |     |    | ||||  ||||| || ||||||||||||||||||||||| ||||||||||||||||  |||||||| || ||| | ||| |                              
------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG-----------------------------

upper sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ26301 (Selaginella moellendorffii), 3'ss of exon 4
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                                              | ||   |||   | |  |    | ||   |  || | |||   |     |  |   || | ||||| ||||| |||||  ||||||||||||||||| |||||||||||   || || ||||| || ||||||||                              
-------------------------------------------------------------gtatactgtcacgcagcgtagccttcat--gtgcttgacatgcccccaatctcgttgcttctttcagGTGGCTACGGAACTTTGGAGGAGCTGTTAGAGGTGATAACATGGGCTCAGCTCGGAATCCACGACAAGCCG-----------------------------

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|58592728|gb|CF991036.1|CF991036
EST:     GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTG                         CGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
genomic: GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTGgtaattgata ... tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcacactagtaattgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG
                                       tattgat  putative branch site (score: 3)
                                             tttttatc  CT-rich tract
            taattgataattcaaa  TA-rich tract