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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag

Basic information

species Oryza sativa
transcript LOC_Os02g54340.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 3
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttctt--ccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag
| || ||||||||||| || ||| |||| ||||| ||||| |||||| | || |||||||| ||||||||||||||||| |||||| | |||||||||    | |||    |       ||| |  |     ||  ||| | || |||| |  ||  |     ||||||||||   |  | |   |  |||   | || | |||||  | | ||   | |  | | | ||  | | || ||| || || ||
GTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAAgtatattaaatgaccctgatattgtgttacttcgtagattttacttttacagctttgagt-tatgacctaccatgcatgatagttg-gtagaaatctttttggtttcaattttacatgtgct---agtgcattaataacttctctttctctttctgcag

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G01810.1 (Glycine max), 5'ss of exon 3
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag
| || ||||||||||| |||||  | ||| |||| ||||| |||||||| || || |||||||| |||||||| |||||||| || || || ||| ||   ||    | || |   |   |  || ||||  || ||      | | |  || |||    | |   |||     | |      ||                                                                
GTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAGgta-attattttttgttttacttggtagaatttgttccaagtgtt-----ctgtatatct-gcaggaattaactatggctatttattgaacag----------------------------------------------------------------

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 3
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttc-cttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag
| || || ||||| ||||| |||||||||   || || || |||||||| |||||||||||||||||||||||||| || |||||  |||| ||   |   |   ||         | | | |||||   | || | |  |   ||| |  ||  | || ||     | |     |||  |||||  ||      | | |                                                  
GAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAGgttagttaatc--ccagccaggttgtcaaacttctcgacatgatctcgtgcatttcttact--cgtatttagcagacgggtggtaataacttaatttattaattgtggcag-----------------------------------------------

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ13722 (Selaginella moellendorffii), 5'ss of exon 3
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatc-gcttaacctatttccccgcctaccttcttccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag
|||| |||||||| |||||||| || ||| | || ||||| |||||||| || || |||||||| ||||||||||||||||| || |||||||||  |  | ||    | ||    | | | | ||  |  ||  | | ||   ||||    | | |                                                                                             
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaagtgagatttttttcttcgatctcttgcttttcttttttctctcatg--tttggttttggtag--------------------------------------------------------------------------------------------

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ29161 (Selaginella moellendorffii), 5'ss of exon 3
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag
|||| |||||||| |||||||| || ||| | || ||||| |||||||| || || |||||||| ||||||||||||||||| || |||||||||    |   |   | ||   |   |||     || ||  | ||     ||| ||                                                                                                     
GGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAAgtaag--ggagatttttttcttcgatctattgcttttctcatgttttggttttggtag---------------------------------------------------------------------------------------------------

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|88302490|gb|CI668336.1|CI668336
EST:     GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
EST: gi|58603359|gb|CK013887.1|CK013887
EST:     GGGATCTAGTATCGGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
EST: gi|88372910|gb|CI640361.1|CI640361
EST:     GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCT
EST: gi|29684844|gb|CB681119.1|CB681119
EST:     GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
EST: gi|88310318|gb|CI659108.1|CI659108
EST:     GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATG
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATG
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     GGGATCTAGTATCGGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
EST: gi|58602175|gb|CK012703.1|CK012703
EST:     GGGATCTAGTATCGGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
EST: gi|88326660|gb|CI658382.1|CI658382
EST:     GGGATCTAGTATCAGATAACCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGT
EST: gi|58675342|gb|CK064029.1|CK064029
EST:     GGGATCTAGTATCGGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
EST: gi|88574346|gb|CI666115.1|CI666115
EST:     GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAA                         GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT
genomic: GGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATAT

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), 68 (downstream exon)
Score: 44

GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgct ... ccttttgaagGTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATTAAGGAGTCTGACACTGGGCTGGCACCACCCAGCCAATGGGATCTAGTATCAGATAAGCAGATGATGCAAGAAGAGCAACCGCTGCAAgtatatcgcttaacctatttccccgcctaccttcttccttgttttaatagttttgtgcctagcatacttcatgcatgatgcctaaggacttagatttcctgctttagttttatgtcttctgtgattttactgacaagatattttcctccttttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA