Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagaatattctgctcagattattggacatatgtagaattgtagataccaatgaaaagctagctggttctcgcactgatgtatggctatttactttactctttgttcattttcagATCAAGGCTGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTGATCAAGGAGGTGACCAATGCAGCTTACAAAGATATAGAAGATGTGGTTGCATTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g03560.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g03560.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G019225_T01 (Zea mays), 3'ss of exon 4
gtaagtagaatattctgctcagattattggacatatgtagaattgtagataccaatgaaaagctagctggttctcgcactgatgtatggctatttactttactctttgttcatttt-cagATCAAGGCTGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTGATCAAGGAGGTGACCAATGCAGCTTACAAAGATATAGAAGATGTGGTTGCATTTG
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gtaagtagtgagttcagtctagcttattggaaatctggtga-ccatacaaacagctctaatg--ggctggttctggcactaac-----agtattt-tgtaactttttatttaatttgcagATCAAGGCAGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTAATCAAGGAGGTGACTAGTGCAGCCTACAAAGATATCGAAGATGTGGTTGCATTTG
upper sequence: LOC_Os08g03560.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G10800.1 (Glycine max), 3'ss of exon 4
gtaagtagaatattctgctcagattattggacatatgtagaattg---tagataccaa---tgaaaagctagctggttctcgcactgatgtatggctatttactttactctttgttcattttcagATCAAGGCTGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTGATCAAGGAGGTGACCAATGCAGCTTACAAAGATATAGAAGATGTGGTTGCATTTG
| || |||| |||| || || || || | | | || | ||| | | | |||| | ||| | | ||| | | | |||| ||||| ||| |||||||||| || ||||||||||| |||||||| | ||||||| |||||||| ||| | | ||||| ||||| || |||||||
------------------------ttttaagcatacatagaggtggcttacttagtaaatttattgaatttatgatttgcctcacatctctgtagctaataactgt-cccttgatatgtatgtagATAAAGGCAGATATTGAGACTCAGGGAGAATTTGTGAATTCATTGATTAGAGAGGTGAACAATGCAGTTTATCAGAACATAGATGATGTAGTGGCATTTG
upper sequence: LOC_Os08g03560.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0003g05680.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtagaatattctgctcagattattggacatatgtagaattgtagataccaatgaaaagctagctggttctcgcactgatgtatggctatttactttactctttgttcattttcagATCAAGGCTGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTGATCAAGGAGGTGACCAATGCAGCTTACAAAGATATAGAAGATGTGGTTGCATTTG
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---------aaattggaatataactagaagttgctgcttgaat---aggtttcaacgagtt-ttagttga--ccagttcagatcttt--ttgtttacaattgtcattgtgtat--gcagATAAAGGCAGATGTTGAGACTCAAGGAGAATTTGTGAACTCTTTGATAAGAGAGGTCAATAATGCAGTTTATCAGAACATTGAAGATGTTGTTGCATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctggttctcgcactgatgtatggctatttactttactctttgttcattttcagATCAAGGCTGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTGATCAAGGAGGTGACCAATGCAGCTTACAAAGATATAGAAGATGTGGTTGCATTTG
cactgat putative branch site (score: 3)
ctttactctttgttca putative PPT
tatttacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagaatattctgctcagattattggacatatgtagaattgtagataccaatgaaaagctagctggttctcgcactgatgtatggctatttactttactctttgttcattttcagATCAAGGCTGATGTTGAGACTCAAGGTGAATTTGTGAAATCATTGATCAAGGAGGTGACCAATGCAGCTTACAAAGATATAGAAGATGTGGTTGCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG