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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatttttatttacgcaatatttgtagattttctgctaagtaatagcaaagtggaaccc...

Basic information

species Oryza sativa
transcript LOC_Os03g15120.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA18G12920.1 (Glycine max), 5'ss of exon 18
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatt--------tttatttacgcaatatttgtag-attttctgctaagtaatagcaaagtggaaccc
|| || || ||  |||| || || || || ||||||||||| ||||||||||||||  | |||||||| |||||||| ||||||||||| |||||||| ||||  |  ||  || || |   || ||   |||  ||| | | ||         ||| |||      | |||| |  | ||  |  | |   | ||| || |||     
GGGGGACGAGAGGGCCGGCCAATTGGTGCTTATGAACTAGCAAAAGCAGTTGAAGAGCTTGGTGCTGGTGAAATACTACTTAATTGCATCGATTGTGACGgtaaat--ataattctgtatcctttaactatat-tttttcttcatcaagagcagtttgtttttttcttctttgaaacacttggtttttaacta-agccaaatgg-----

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA18G10460.1 (Glycine max), 5'ss of exon 18
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatttttatttacgcaatatttgtagattttctgctaagtaatagcaaagtggaaccc-----
|| || || ||  |||| || || || || ||||||||||| ||||||||||||||  | |||||||| |||||||| ||||||||||||||||| || ||||  |  ||  || || |   || ||   |||  ||  |   ||||||  ||   ||| |   ||   |||| | ||   |   | ||   |||          
GGGGGACGAGAGGGCCGGCCAATTGGTGCTTATGAACTAGCAAAAGCAGTTGAAGAGCTTGGTGCTGGTGAAATACTACTTAATTGCATTGATTGCGACGgtaaat--ataattctgtatcctttaac--tatatttcactatattttttcttcatcaagagcagtttgtttttttcttctttgaaacact-tggtttttaacta

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT4G26900.1 (Arabidopsis thaliana), 5'ss of exon 17
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatttttatttacgcaatatttgtagattttctg--ctaagtaatagcaaagtggaaccc---
|| || || ||  | || ||||| ||||||| ||| || || ||||| ||||||||||| ||||| || ||||||||  | || ||||| || ||||||||||   |||    ||  | |  ||  |  |  |    || ||||     ||||   | |  |||  | |   |  |  |||| ||  | | | |   |||     
GGAGGACGAGAAGGTCGACCTATTGGAGCATTTGAGCTTGCGAAAGCGGTTGAAGAATTAGGTGCCGGTGAAATACTATTGAACTGCATAGACTGTGATGgtacactcaaaacttcaatc--tttgaattagtttcatgtctgaaa---atttggaccacctttacacacgatgagaactaaatatgatccacgaaaaacaaaaa

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv19s0090g00810.t01 (Vitis vinifera), 5'ss of exon 16
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttc-aatattatgctttgcctgatttttatttacgcaa-tatttgt-----agattttctgctaagtaatagcaaagtggaaccc
|||||||| ||  |  | || || ||||| ||||| || || ||||||||||||||  |||| |||||||||||||| || || |||||||||||||||||  || | |||  |   |     |  || | |||   || | || | ||  |  | |||| | ||| |     | ||| |||   || |  || |||||        
GGTGGGCGAGAAGGTAGACCAATTGGAGCTTATGAGCTTGCAAAAGCAGTTGAAGAGCTGGGAGCTGGAGAAATACTACTCAACTGCATTGATTGTGATGg--tgataatgactcctagttccttgaaaaatatctgtttcatgttattattgaatgcaaatttttatctgaaaaattctctaggaaatggtaacaaagact-----

upper sequence: LOC_Os03g15120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S43_232V6.1 (Physcomitrella patens), 5'ss of exon 16
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatttttatttacgcaatatttgtagattttc-tgctaagtaatagcaaagtggaaccc
||||| || |||||  | ||||||||||||||||| || |||||||||||| ||||  | |||||||| ||||| ||  | || |||||  ||||||| |||| |    | | | |   |  || |  |   |  |||   ||  ||| |||    |  | | ||    | | |  |  | | ||   |||     |    
GGTGGCCGCGACAGGAGACCTATAGGAGCATATGAGCTTGCCAAAGCAGTTCAAGATCTTGGTGCTGGGGAAATTCTCTTGAACTGCATCAATTGTGACGgtacgggt-ttgctctactctttttatcagacttgtttttgtggctttcattacgtctttgtgtgccagtatgcacggcatgcaaagtcaatacaaagtgt

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|86504136|gb|CI146769.1|CI146769
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|89164031|gb|CI101119.1|CI101119
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88438607|gb|CI543711.1|CI543711
EST:     CATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: CATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88265787|gb|CI376689.1|CI376689
EST:     TGAAGAATT-GGTGCTGGAGAAATACTTCTTAAGTCCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88531682|gb|CI460092.1|CI460092
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTNTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|86600373|gb|CI356130.1|CI356130
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88907823|gb|CI091221.1|CI091221
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88515936|gb|CI443590.1|CI443590
EST:     ATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: ATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|87010113|gb|CI279210.1|CI279210
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88552745|gb|CI482783.1|CI482783
EST:     ATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: ATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|33808918|gb|CF330345.1|CF330345
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88978697|gb|CI385038.1|CI385038
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|86500063|gb|CI142696.1|CI142696
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|86432146|gb|CI085757.1|CI085757
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88221798|gb|CI221754.1|CI221754
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|86597766|gb|CI274757.1|CI274757
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|87016640|gb|CI275642.1|CI275642
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
EST: gi|88849245|gb|CI087767.1|CI087767
EST:     TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATG                         GCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG
genomic: TGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTG

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: 73 (upstream exon), 72 (downstream exon)
Score: 7

GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcat ... tatttttcagGCCAGGGCTGCGGATTTGACATAGATCTGGTAAAAATGGTGTCAGATGCTGTGACTATCCCTGTCATTGCAAGCAGTGGTGCTGGTACTGTCGAACATTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGGCGTGACAGCCGTCCTATAGGAGCATATGAACTAGCCAAAGCAGTTGAAGAATTGGGTGCTGGAGAAATACTTCTTAATTGCATTGATTGTGATGgtatgttcatggttttgaacagttcaatattatgctttgcctgatttttatttacgcaatatttgtagattttctgctaagtaatagcaaagtggaaccc

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA