Sequence
atgc intronic sequence ATGC exonic sequenceTTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaatatttttagttgactgcaactaggattatattggcttcttatgtgtaaaaccattttcttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g16824.3 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA09G15200.1 (Glycine max), 5'ss of exon 17
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagc----------acaatatttttagttgactgcaactaggat-tatattggcttcttatgtgtaaaa----ccattttcttcag------------
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TATCTAGAGATCCATCTCTTTTGGGCTGGAAAAGGGACTTGTTGTATACCAGTTCAAGGTACTTATGGGCCCCTGATTTCAGCCATTAGTGCTATCCCAGgtaaaacttaaaagagacaggcttttcatatatttggtccaaacacatacgtgaaaatgttgttttttatttttcctatttttgctagtcattatagtaa
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA08G25590.1 (Glycine max), 5'ss of exon 20
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaatatttttagttgactgcaactaggatta--tattggcttct---tatgtgtaaaaccattttcttcag------------------------------------------------------
| ||||||| ||||||||||||||||| ||||| |||||||| |||| ||||||||| || || || || |||| | | |||| |||| || || | ||| | | ||| || | | | | |||| ||| || | | ||
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATTCCAGgtaa-tactatgaaaaaaattggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatttttttaatttgatacattgttttgtgttgtacag
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA08G25600.1 (Glycine max), 5'ss of exon 17
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaa----gcacaatatttttagttgactgcaactaggatta-tattggcttcttatgtgtaaaaccattttcttcag------------------------------------------------------
| ||||||| ||||||||||||||||| ||||| |||||||| |||| ||||||||| || || || || |||| | | ||| |||| || | ||| || | | | |||| || | ||||| ||| || | | ||
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATCCCAGgtaatactatgaaaaaaatttggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatatttttaatttgataaattgttttgtgttgtacag
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 5'ss of exon 43
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaag-----cacaatatttttagttga---ctgcaactaggattatattggcttcttatgtgtaaaaccattttcttcag-----------
| |||||| |||||||||||||||||||| ||||| ||||| ||||||||| ||||||| || ||||| | || |||||| | || || |||||||| | || | ||| | | | | ||||| || | | | | || | | | | | |
TACATTGAAATCCATCTCTTTTGGGCTGGAAAAGGGACTTGCTGTGTACCTGCTCAAGGGACATATGGACCTTCTATTTCAGCAATCAGTGCTACCCCAAgtaatgtaattagaaactatttgatgcaaatcagtaactaaaatgttgatctactttcatactgatactgaatgattgctaaatttacacag
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 5'ss of exon 18
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaa-------gcacaatatttttagttgact-gcaactaggattatattggcttcttatgtg-----taaaaccattttcttcag--
| |||||| |||||||||||||||||||| ||||| ||||| ||||||||| ||||||| || ||||| | || |||||| | || || ||| |||| | | ||||| | | | ||||| || | | | | || | | || | || | ||
TACATTGAAATCCATCTCTTTTGGGCTGGAAAAGGGACTTGCTGTGTACCTGCTCAAGGGACATATGGACCTTCTATTTCAGCAATCAGTGCTACCCCAGgtaatgcaattggaagctatttgatgcaaatcagtaactaaaatgttgatccactttcatactggtactgagactaaattttacacag
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv12s0055g00580.t01 (Vitis vinifera), 5'ss of exon 18
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaag-----cacaatatttttagttga---ctgcaactaggattatattggcttcttatgtgtaaaaccattttcttcag-----------
| |||||| |||||||||||||||||||| ||| | ||||| ||||||||| ||||||| || ||||| | || |||||| | || || |||||||| | || | ||| | | | | ||||| || | | | | || | | | | | |
TACATTGAAATCCATCTCTTTTGGGCTGGAAAAAGGACTTGCTGTGTACCTGCTCAAGGGACATATGGACCTTCTATTTCAGCAATCAGTGCTACCCCAAgtaatgcaattagaaactatttgatgcaaatcagtaactaaaatgttgatccactttcatactgatactgagtgattgctaaatttacacag
upper sequence: LOC_Os05g16824.3 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv12s0055g00660.t01 (Vitis vinifera), 5'ss of exon 8
TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaag-----cacaatatttttagttga---ctgcaactaggattatattggcttcttatgtgtaaaaccattttcttcag------------
| |||||| |||||||||||||||||||| ||||| ||||| || |||||| ||||||| || ||||| | || |||||| | || ||| ||| |||| || || | ||| | | | | ||||| || | | | | || | | | | | |
TACATTGAAATCCATCTCTTTTGGGCTGGAAAAGGGACTTGCTGCGTACCTGCTCAAGGGACATATGGACCTTCTATTTCAGCAATCAGTGCCACCCCAGgtaacgcaatcagaaactatttgatgcagatcagtaactaaaatgttgatccactttcatactgatactgagtgattactaaattttacacagMapped 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|58679752|gb|CK068439.1|CK068439EST: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAA ATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAG
genomic: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaa ... ttttcttcagATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAG
EST:
gi|218482657|gb|FG955336.1|FG955336EST: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAA ATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAG
genomic: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaa ... ttttcttcagATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAG
EST:
gi|29627080|gb|CB632091.1|CB632091EST: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAA ATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAG
genomic: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaa ... ttttcttcagATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAG
EST:
gi|88383614|gb|CI543387.1|CI543387EST: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAA ATTTTACTCCCACTGTACGGAATGGGGTACC
genomic: TACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaa ... ttttcttcagATTTTACTCCCACTGTACGGAATGGGGTACC
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),
63 (downstream exon)
Score:
17TTCATTGAGATCCATCTCTTTTGGGCTGGCAAAGGCACTTGTTGTGTACCTACTCAAGGTCACTACGGACCGACGATCTCAGCATTAAGCATCACTCCAAgtaagcacaa ... ttttcttcagATTTTACTCCCACTGTACGGAATGGGGTACCAAAAAAGAGAAGTAAAGCAGGTGCAATTGTTGGAATAGTGATTGGTGCATCAGTTTTAGGATTGGCAGC
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