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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

Basic information

species Oryza sativa
transcript LOC_Os09g19700.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||||| ||||| |||||| | | || | || ||| |||| ||| | ||| |||| | || | |||| || |||||||||||||| |||||||||||||| ||||| || ||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||
-------gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||||| ||||| |||||| | | || | || ||| | || || | | ||| |||| | || | ||||| || || ||||| ||||| |||||||||||||| ||||| || ||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||
-------gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
|||||| | || || ||| |||| | | ||| | || || | || || ||| ||| | ||||| |||||||| || |||||||||||||| |||||||||||||| || | |||||| ||||| || |||||||||||||| |||||||| ||||||||||
gtaagtgtcaaaaactacaataagattgcat----------------ttcccccttttta--tcagtctaatattgtaccgattcagGAGTACAATGCCAAGCTCTCAGATTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G05260.1 (Glycine max), 3'ss of exon 3
---gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||| || | | || |||| | | | || ||| ||| ||| | || || | || || |||| |||||||||||||| || || ||||||||||| |||||| || || || || |||| |||||| || ||| ||||||||||||| | |||||||
gtaataacttgaatattgtttcattgcttactatgctaactttcaacagataaacacctttacctgcatcttaacatcattctgttttagGACTACAATGCAAAACTTTCTGACTTTGGGCTTGCGCAAGATGCTCCAGTGGGAGATAAAAGTCACGTTTCCACTGAAGTAATGGGAACACAAGGTTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||| || || ||| | || ||| | | || | | || | | | | | || |||| |||||||| |||||||| |||||||| || ||||||||||| |||| ||| || || || ||| | || || |||| |||||||||||||||||||
gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgttttt--agGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
|||||| || | || |||| ||||| ||| | || | | ||| ||| |||||||| || | ||||| |||||||| || |||||||| ||||| ||||| |||||||| || | ||||| |||||||| |||||||||||||| |||||||| ||||||||||
gtaagtgccaaatt-ttaaatt--attac-catttttcttttcat--tccttgatttg---atttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttg--taattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||||| ||| | | | |||| | || | | |||| |||| | | | |||||||| || | ||||| |||||| | || |||||||||||||| ||||| |||||||| || | ||||| ||||| || |||||||||||||| |||||||| ||||||||||
-------gtaagtggccaaat--gttaagttattac-catctttcttttcattccttgatttgatctttatattattataacaattcagGAATACAATTCTAAGCTCTCAGATTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
| || || | ||| |||| | || || | | | | | ||| | | | | | || |||| |||||||| || || || |||||||| |||||||||||||| |||| || || || || || || ||||| |||| |||||||||||||||||||
---gtatgtaggtgaaggtatta-attatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaa---atgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
|||||| || ||| |||| | |||| | | | |||| | | | ||||| | | | ||||| |||||||| || |||||||| ||||| |||||||||||||| || | |||||| ||||| || ||||||||||| || |||||||| |||||||| |
gtaagtgcccgaaactacaataagattgcatatttcctcct------------ttttgttagtcta-atattgccccaatt---cagGACTACAATGCCAAGCTCTCAGACTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGGGTGATGGGAACCTATGGTTACG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
-gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||| || || ||| | || ||| | | | || | | || | | | | | || |||| |||||||| || ||||| |||||||| || ||||||||||| |||| ||| || || || ||| | ||||| |||| ||||||||||||||||||
ggtatgtgagttaaccaggaaaaaggtttttaattattttctatccatcctccaacataaaaacataaaaacataattgttttt--aGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G02730.1 (Glycine max), 3'ss of exon 3
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
|||| | || |||| | || | || || ||| ||| | || ||| | || || |||| |||||||||||||| || || |||||||||||| |||||| || || || || |||||||| || || ||| ||||||||||||| | || ||||
gtaataacttgaatgttccattgcttactatactaactttcaacatataaacacctttacttacctcttaatatcattctattttagGACTACAATGCAAAACTTTCTGACTTTGGGCTTGCCCAAGATGCTCCAGTGGGAGATAAAACTCATGTTTCCACTGAAGTAATGGGAACACAAGGCTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgta--tattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
|| | | | |||| || | ||| | | || | |||||| || | || | | ||||| |||||||||||||| ||||||||||| ||||||||||||| |||| | | |||||| || || |||||| | || ||||| |||||||| ||||
-----------gtacgtatctc---ttactctttaggatcaacat--cttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G01300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttaag--tccttgaatt---ggatta-cgtattgcacac-cacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||| ||||| || || || |||| | | | || | || | | ||| ||| ||| | || ||| | || ||||| |||||||| ||| | ||||||||||||||||||||||||| |||| | | ||||||||| |||||||||||||| ||||| || |||||||| |
gtatgttttcctcttctttatatcaagggatcaacatcttatatacacgtctgtttctttgcttctaaagtcttac--catgtcccaatttcagGAGTACAATGCTAAATTATCAGATTTTGGGCTTGCCAAAGATGCTCCTGATGAAGGCAAAACTCATGTGTCTACTCGAGTCATGGGCACTTATGGTTACG

upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttttaagtcc-ttgaattggattacgt-attgcacaccacacgattcacatcttgtaatttt-gtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
||| || | || || | || ||| || | | | || | | | | | |||||| | | | ||||| | |||||||| || |||||||| ||||| |||||||||||||| ||||||| || | | | ||| | ||||| || || ||||| |||||||| ||||||||||
gtatgtctgaaagccacttaacccgataacctcaactctgtcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

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|3761134|gb|C98382.1|C98382
EST:     TGATTTTAAAACATCTAATATACTGCTAGATGCT                         GATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
genomic: TGATTTTAAAACATCTAATATACTGCTAGATGCTgtaagtttta ... actcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
EST: gi|163929492|gb|EG709283.1|EG709283
EST:     GACCAGTTATTTACCGTGATTTTAAAACATCTAATATACTGCTAGATGCT                         GATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
genomic: GACCAGTTATTTACCGTGATTTTAAAACATCTAATATACTGCTAGATGCTgtaagtttta ... actcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA

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: 75 (upstream exon), 75 (downstream exon)
Score: 29

TGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTACCGTGATTTTAAAACATCTAATATACTGCTAGATGCTgtaagtttta ... actcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
                                           ctactctt  CT-rich tract
 atcttgtaattttgta  TA-rich tract