Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaattattgcatcaacaataagcaattcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaacagGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g02670.2 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g02670.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G024576_T02 (Zea mays), 3'ss of exon 16
gtatgttaattattgcatcaacaataagcaattcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaacagGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG----------------
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----gtgctttattgcacgaacctcatgccgtgcgctgtgtgttaatg-atctcgcagcatagcataattttattacctttaacagGAGTGCGCAGCTAATGAAGAAAAACAGCTTCTAGAGAAGGTGGCGGAGATGCTGGCAAGTTCCAACGCACGGAAGAAGAAGCTGGTGAGCGTTTTTTTTT
upper sequence: LOC_Os05g02670.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 16
gtatgttaattattgcatcaacaataagcaattcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaacagGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
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----gtgctttattgcacgaacctcatgccgtgcgctgtgtgttaatg-atctcgcagcatagcataattttattacctttaacagGAGTGCGCAGCTAATGAAGAAAAACAGCTTCTAGAGAAGGTGGCGGAGATGCTGGCAAGTTCCAACGCACGGAAGAAGAAGCTG
upper sequence: LOC_Os05g02670.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 16
----------------gtatgttaattattgcatcaacaataagcaa----ttcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaac-------agGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
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gtgattgcagtagtgccttttctgagaattacataaatcatgatcagaaattttttgcacttgt-tttttttttctaacctttgatgctctcctcattctttactgggtgaagGAGTGTACTGCCTATGAAGAAAAACAACTACTGGAGAAAGTGGCAGAAATGCTAGCAAGTTCTAATGCTAGAAAGAAACAGTTG
upper sequence: LOC_Os05g02670.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA13G40580.1 (Glycine max), 3'ss of exon 17
-------------gtatgttaattattgcatcaacaataagca--attcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaac-------agGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
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gtgattgcagtgccttttctgagaattacataaatcatgatcagaaatttttagcacacatttt--ttttttctaacctttgatgctctcattctttactgggtgtagGAGTGTACTGCCTATGAAGAAAAACAACTACTGGAGAAAGTGGCAGAAATGCTAGCAAGTTCAAATGCTAGAAAGAAACAATTG
upper sequence: LOC_Os05g02670.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA11G15520.2 (Glycine max), 3'ss of exon 16
-----------------gtatgttaattattgcatcaacaataagc---aattcataagctaatattttgttttgtgtcaat----atgtaattttgccattttaaac--agGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
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gtgatcgaagtgtgcctttttgcagaat-ttgcataaatcatgatcggaaaatttttaattaatactcccttcttttttaactttgatgcatcttattctttatgggtgtagGAGTGTACTGCGCATGAAGAAAAACAACTACTGGAGAAAGTGGCAGAAATGCTTGCTAGCTCTAGTTCTAGAAAGAAAAAACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaacagGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
agctaat putative branch site (score: 3)
ccatttt putative PPT
taatattttgttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaattattgcatcaacaataagcaattcataagctaatattttgttttgtgtcaatatgtaattttgccattttaaacagGAGTGTGCAGCTAATGAAGAAAAACAACTTCTAGAGAAGGTGGCAGAGATGCTTGCAAGTTCCCATGCAAGGAAGAAGAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG