Sequence
atgc intronic sequence ATGC exonic sequencegtaagatttttttttttgtggatgaactatttgcagaagtgctagaactgatttttggattagcatgccgttggaacagcatttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g16090.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g16090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G160198_T02 (Zea mays), 3'ss of exon 6
gtaagatttttttttttgtgga----tgaactatttgca----gaagtgctagaactgatttttggattagcat-----------gccgttggaacagc---atttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
||||| | | | | | | ||| | || |||| | || | || | | ||||||| ||||| ||| || || ||| | | || | | || | || ||||||||||||||||| ||| ||| |||||||||||||||||||| || |||||||| ||||||||||| |||| |||||||| || || || || |||||||
gtaaggcctcgtgtcctcggaaaacctgagcgatctgcactgcagactgtgataaactgcgtacgcgttagcatttctacgccgtgccgtctcgtcagtgtaatgagctagaagctcattctttctagatg--tgtttctgcagATCCCAACGAACGGGAGTGGCTTGATAGAGTACAGAGCCCACCCGTTCTGGGGCCAGAAGTATTGCCCTTCGCATGAGCGCGACAGGACGCCACGTTGCT
upper sequence: LOC_Os03g16090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G151934_T02 (Zea mays), 3'ss of exon 6
gtaagatttttttttttgtggatgaactatttgcagaagtgctagaactgatttttggattagcatgccgttggaacagcatttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
||||| || | | ||||| | ||||| || | |||| | | || ||| | | | | |||| ||| ||| | | || | |||| | || ||||||| ||||||||||||| ||| ||||||||||||||||||| || |||||||| ||||||||||| |||| ||||||||| || || || || |||||||
gtaaggcttcatctgaaacc--tgaacgaccagcagac-tgacaaaact-acatatgcgttaacgtttctgtacttggtcatt-gcaagaagctcattcttttcctttgtctgtttctgcagATTCCAACGAACAGGAGTGGCCTGATAGAGTACAGAGCCCACCCGTTCTGGGGCCAGAAGTATTGCCCTTCGCATGAGCACGACAGGACGCCACGTTGCT
upper sequence: LOC_Os03g16090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G160198_T01 (Zea mays), 3'ss of exon 6
gtaagatttttttttttgtggatgaactatttgcagaagtgctagaactgatttttggattagcatgccgttggaacagcatttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
| | | ||| | | | | | | | | ||| | | || || ||| | | || | | || | || ||||||||||||||||| ||| ||| |||||||||||||||||||| || |||||||| ||||||||||| |||| |||||||| || || || || |||||||
----------------------------------gtacgcgttagcatt--tctacgccgtgccgtctcgtcagtgta--atgagctagaagctcattctttctagatg--tgtttctgcagATCCCAACGAACGGGAGTGGCTTGATAGAGTACAGAGCCCACCCGTTCTGGGGCCAGAAGTATTGCCCTTCGCATGAGCGCGACAGGACGCCACGTTGCT
upper sequence: LOC_Os03g16090.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ07250 (Selaginella moellendorffii), 3'ss of exon 2
gtaagatttttttttttgtggatgaactatttgcagaagtgctagaactgatttttggattagcatgccgt-tggaacagcatttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
| ||| | | || | || ||| | || | | || || ||||| ||| |||| |||| ||||||||||| | || ||||| ||||||||||| |||||||| || |||||||| | || || ||||| || |
--------------------------------------------------------------gtatgttttgttgagctttatatgcggatggtatttact-----tccagtcatt----cagATTCCACCGAATTCCTCTGGCCTGATAGAGTACCGCGCACATCCTTTCTGGGGACAAAAGTATTGCCCCTTGCATGAAAAGGACTCCACCCCTCGATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgttggaacagcatttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
tttttatt CT-rich tract
tttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatttttttttttgtggatgaactatttgcagaagtgctagaactgatttttggattagcatgccgttggaacagcatttgcaggaaaccctttttacgtgtttggtttttattgcagATCCCAACGAACAGGACTGGTTTGATAGAGTACAGAGCCCATCCATTCTGGGGACAGAAGTATTGTCCTTTGCATGAGCATGATAGAACACCTCGTTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT