Sequence
atgc intronic sequence ATGC exonic sequencegtattatgcggaaagcaccccccggaaatccgcaaatttcgatccgccacttgttacctaccatacgagtactgattttgccgtttcgtggtggtggccttccctgtccggcaattgactcttagATAGGGTCGGGCACCTATAGCAACGTGTACCGCGCGAGGGACACCGTCTCCGGCCGCATCGTGGCGCTGAAGAAGGTCCGGTTCGACAATCTCGAGCCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g27020.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 1
gtattatgcggaaagcaccccccggaaatccgcaaatttcgatccgccacttgttacctaccatacgagtactgattttgccgtttcgtggtggtggccttccctgtccggcaattgactcttagATAGGGTCGGGCACCTATAGCAACGTGTACCGCGCGAGGGACACCGTCTCCGGCCGCATCGTGGCGCTGAAGAAGGTCCGGTTCGACAATCTCGAGCCCG
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---gtaggcgaaaacctctcccctgaaatctg---gtcgtggtacgg--------aagtacc------gtactgattc-gccattcccttgttgtg-ttggctttgtccggcgattcactcttagATAGGATCGGGCACGTACAGCAACGTGTACCGGGCGAGGGACACCGTCTCTGGCCGGATCGTCGCTCTTAAAAAGGTCCGCTTCGATAACCTCGAGCCAG
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S428_20V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------gtattatgcggaaagcaccccccggaaatccgcaaatttcgatccgccacttgttacctaccatacgagtactg--attttgccgtttc-----gtggtggtggccttccctgtccggcaattg-actctt------agATAGGGTCGGGCACCTATAGCAACGTGTACCGCGCGAGGGACACCGTCTCCGGCCGCATCGTGGCGCTGAAGAAGGTCCGGTTCGACAATCTCGAGCCCG
|| || | || || | ||| | | ||||| | | | || | | ||| || |||| ||| | | || || | ||| || | | |||| || ||| || || |||||||||||| || ||||| | | || |||||||| ||||||||||||||||||||||| | ||||| |
gtgagtgggctccggttgcaatgcatttcaatgtgttgatgacagtgagtcgtgtttt-tagacgatggcctctggatg-cagtgaattt-ggtgaatgggcgatggaggggcacgaggggcctgggatgttgcaaattctgaaggcgagaatgaagcattaaccatggaatttgcacacgttggtgcagATTGGACAGGGAACGTACAGCAACGTGTACAAAGCTCGGGACCTAGAGACAGGGAAGATCGTGGCTCTGAAGAAGGTCCGGTTCGACAACTTAGAGCCAG
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S271_84V6.1 (Physcomitrella patens), 3'ss of exon 1
gtattatgcggaaagcaccccccggaaatccgcaaatttcgatccgccacttgttacctaccatacgagtactgattttgccgtttcgtggtggtggccttccctgtccggcaattgactc--ttagATAGGGTCGGGCACCTATAGCAACGTGTACCGCGCGAGGGACACCGTCTCCGGCCGCATCGTGGCGCTGAAGAAGGTCCGGTTCGACAATCTCGAGCCCG
|| | | || | | | | | | | || | | | || | | ||| | | || || || | | || | | | |||| ||| ||| || || |||||||||||| ||| |||| | | || |||||||||||||||||||| || |||||||| || ||||| |
-----gtgagtggggatggtagtgggggtgcagggaatgtggggagtggat-gtgatggagcg---gaatgc----------gttgtggagggggagcattaacagggtgggtgtgggtgggatcagATTGGGCAGGGAACGTACAGCAACGTGTACAAAGCGCGGGATCTGGAGACGGGGAAGATCGTGGCGCTGAAGAAGGTTCGATTCGACAACCTGGAGCCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgattttgccgtttcgtggtggtggccttccctgtccggcaattgactcttagATAGGGTCGGGCACCTATAGCAACGTGTACCGCGCGAGGGACACCGTCTCCGGCCGCATCGTGGCGCTGAAGAAGGTCCGGTTCGACAATCTCGAGCCCG
ctctt CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattatgcggaaagcaccccccggaaatccgcaaatttcgatccgccacttgttacctaccatacgagtactgattttgccgtttcgtggtggtggccttccctgtccggcaattgactcttagATAGGGTCGGGCACCTATAGCAACGTGTACCGCGCGAGGGACACCGTCTCCGGCCGCATCGTGGCGCTGAAGAAGGTCCGGTTCGACAATCTCGAGCCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG