Sequence
atgc intronic sequence ATGC exonic sequencegtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g41120.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G161019_T04 (Zea mays), 3'ss of exon 6
gtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
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-------------------------------------------------------------------------------------------------------------------------------------------------------gTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G161019_T04 (Zea mays), 3'ss of exon 5
gtatgcacaatcttttctaatgggaatgtattttgttt-atacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
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gtatgcacacctttttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttgcttggaccta-------------ctctgagct-cagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAA------------------------------------------------------------
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G161019_T01 (Zea mays), 3'ss of exon 5
gtatgcacaatcttttctaatgggaatgtattttgttt-atacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
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gtatgcacacctttttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttgcttggaccta-------------ctctgagct-cagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 5
gtatgcacaa---tcttttctaatgggaatgtattttgtttatacctc-ttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggcttt-------ctggac--ttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
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gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttact---tctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
gtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
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-----------actgtgtatttgtacactttcatgtcagtgcaacttat-actccaatcgttt---ctttatttcttatatgtc-tatgctttctct--atcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
upper sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
gtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgt-tacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
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-------------tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtt--tcttaatttcttatacgtctatgctttttctctcactcgttctcatg----cagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
ttctaac putative branch site (score: 1)
ctttct putative PPT
tttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG