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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA

Basic information

species Oryza sativa
transcript LOC_Os05g46360.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46360.2 (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--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
                                     |||||| | ||| ||      ||| ||||||     ||| |    | ||| || ||| | | |  || ||| ||   |   | | |   | |  |     |||||| ||  |        | | | ||| |  |||||          || | || ||| || |||||||| ||||| |||||||| ||||||||||| |||  |||||||||||| ||| | || || 
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG

upper sequence: LOC_Os05g46360.2 (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--------tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
                                       |||||||| ||| ||     ||| ||||||     ||| |    | ||| || ||| | | |  || |||  |  |||  | | |   | |  |     |||||| ||  |        | | | ||| | ||||||          || | || ||| || |||||||| |||||||||||||| ||||||||||| |||  |||||||||||| ||| | || || 
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgtattgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG

upper sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------gtaat-tgataattccaatatatgtgag-----atggactgacgatctgaaatgttca-gtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaa---cttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
                                                           | |  || ||||   | || |  ||       ||  |||||  || |   || || | |||| |  || ||   ||  | ||| | | ||||| ||  || |||     ||    ||   | |||   || ||  ||| || |||||||| ||||| |||||||| ||||||||||| |||   ||||||||||||||| | || || 
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactga-aatttactattttgatgtacttgattgctg-tattgtgtat-ataatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG

upper sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttca-gtaccttctttcta-acatcatctatcacactagtaattgataatt-caaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
                                                                || | || |  |    || |   |   ||  |||||  || |   || || | ||||    || ||  |   ||| ||| | |  | | | |  |  || |  ||      |     ||  || | || ||| || |||||||| ||||| |||||||| ||||||||||| |||   ||||||||||||||| | || |  
gtagttaccacaagagctttcaaatagttttaaaaataattgatgattgtttgtcttatgacatgttaatgttgctaaagatgttctttttatatactga-aatttactattttgatgtactggattgctgtattgcatgtataatagcaattactatttctttcttataccctctctcatttccttataattagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACAG

upper sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatc-tatcacactagtaa--ttgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
                                                 | || |    ||||  |||   ||| || |  | |  |||  |||| | ||    | | |     |    | ||||  ||||| || ||||||||||||||||||||||| ||||||||||||||||  |||||||| || ||| | ||| | 
------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG

upper sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ26301 (Selaginella moellendorffii), 3'ss of exon 4
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA
                                                              | ||   |||   | |  |    | ||   |  || | |||   |     |  |   || | ||||| ||||| |||||  ||||||||||||||||| |||||||||||   || || ||||| || |||||||| 
-------------------------------------------------------------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|38468858|gb|CF952989.1|CF952989
EST:     GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTG                         GGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
genomic: GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTGgtaattgata ... tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
EST: gi|58590993|gb|CF989301.1|CF989301
EST:     GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTG                         GGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
genomic: GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTGgtaattgata ... tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
EST: gi|58591325|gb|CF989633.1|CF989633
EST:     GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTG                         GGGGCGATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
genomic: GCGGAAAGCGGAGATGGCTCGGCGATCCAAAGCGTTCATTGCTCTTCCTGgtaattgata ... tttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAAC
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.

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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatctatcacactagtaattgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG