Sequence
atgc intronic sequence ATGC exonic sequencegtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 2
-------------gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
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gtaatagaggaatttctttagtactacacaacttggaaacctggaattttggtt-----ttgtatcagcaccggagagtaagccgtcttcctttctatcttagGTGGCACTGAAGTTTGAGCATAGGACCAGTAAAGGATGTCACTATGGCCCTCCTTATGAATGGACAGCTTACAA
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatttagtgc-cagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaa-ataaatatcgtgctttcgaatg-gtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
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-------gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 2
gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
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-----------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgtta------taacgctcgtttgc---gcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTACGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtatttagtgccagcctatttgtaaaactgtacttgta-accgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
|| || || | | | || | | | | | | | | ||| ||| | | || | || |||| || | ||||||||||| |||| |||||||||||||||| |||||||||| || || ||||| |||||||
----------gtagactgttcgaagatttgctcagttggattggctcttttctcagcggctgatcaaagatgttgt------------cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
| || | | | | | | | | || | || || | || | | |||| || || ||||| || ||||| | ||| ||||| |||||| ||||||||||||||||||||||||||||| |
-----------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgtta------taacgctcgtttgc---gcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
|| || || | | | | | | | | | | ||| ||| | | || | || |||| || | ||||||||||| |||| |||||||||||||||| |||||||||| || || ||||| |||||||
----------gtagactgttcgaagattttctcagttggattgctcttttctcagcggctgatcaaagatgttgt------------cagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
tattaac putative branch site (score: 1)
tgctttc putative PPT
ttgaaaataaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG