Sequence
atgc intronic sequence ATGC exonic sequence...ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgttctgatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G163473_T01 (Zea mays), 3'ss of exon 4
ggtaaaacat--ctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgttctgatca--cagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
| | | | || ||| | |||| | | || ||| | ||| | ||| ||| || | ||| |||| |||| || ||||| ||||||||||| ||| ||||||||||||||| |||||||||||||||||| |||||||||||| ||||||||||||||||||| ||||| || ||||
--ttacgcgtggctgagatttatattaatttgcattttgcaatattttgtttgtcacgcta-aatgtgcttgacctttga-catatactgctctggtcttccagGATAGGGATCGCAAGCTGCGGATATTTTCTGGAATTGAGCATCCATTCCATGACCGCCCTCTTGAAGCTTTTGTGATGCCACCACGGCAAGTACGGGAGA
upper sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
-ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgttctgatca--cagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
| ||||||| |||| | | | | ||| | ||| | | ||| ||| | || ||| |||| |||| || ||||| ||||||||||| |||||||||||||||||||| || |||||||||||||| |||||||| ||||||||||||||||| ||||| ||||| || ||||
tttcataacatct-tattgtatcatggt-cgaggaatcatgccttttgctggtcacgttaaaatgtgcttggt-gtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
upper sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 5
ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataa-tgctgttgttgcttat-taagcatgcactgttct----gatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
| | || | || | || | || | || | | |||| || | |||| || | | | |||| | || | | | ||||||||||||| ||| | ||||| ||| |||| | |||||| || || ||||||||| |||||||||| ||||||||| || | || || || |
--tcatttggttagaactttttctgat----attttttgttccttataatattgaataactgatattgtaagttgtatttacttgcattattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA
upper sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgt-tctgatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
| | ||| ||||| | || | ||| | | | | | | | ||||| | |||| |||| | | | |||||| || ||||| ||||| ||||||||| |||| ||||||| || ||| |||| | ||||||||||||| ||||||||| || || ||||| || || |
ttttagtcat-tatatgaatgatgtcttgttaactttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagcttcatataatgctgttgttgcttattaagcatgcactgttctgatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
ctgttct CT-rich tract
ttcatataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgttctgatcacagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA
- - aaacatc
- - - - - - - - - tccttca
- - - - - - - - - - - - - - - - - - - - ttgctaa
- - - - - - - - - - - - - - - - - - - - - - - - gcttcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcatgc