Sequence
atgc intronic sequence ATGC exonic sequencegtctgcttcacatatttacattatatgatgatgtttgttgcaggtgcccttgtggagctgaatgttttatgttgttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54020.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 5
gtctgcttcacatatttacattatatgatgatgt--ttgtt--gcaggtgcccttgtggagctgaatgttttatgttg-ttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
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gtctgccttgcatacttgcactgcagtgtgttttgattattctgtacgtgtatgcttctgttcttatgtattatgatgactctttgttctttcagGCTTCTATCTTTGTACAGTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTATTGAGTTCTTCTACTCCTATTGGCTGGCTGAATAGAATGATCCAGT------------------
upper sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G09240.2 (Glycine max), 3'ss of exon 1
gtctgcttcacatattt------acattatatga--tgatgtttgt--tgcaggtgcccttgtggagctgaatgttttatgttgttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
|| | || || ||| || || | || | || ||||| || | || | | || || | | | || || ||| |||||||||| ||||||||||||||||||| || || ||||| || ||||||||||| || ||||| | || || ||||||||||| |||| |||||| ||||
gttctttgcaaatttttctccgaaccttttgggaaataatatttgtggtggaaatgtcaagatcactgtggataaatgacat-gtgttttgtgcatacagGCTTCAGTATTTGTACAGTCTCATGTTCGGGCACATGTAGAATTGATGTGGCTGCTAAGTTCCACAACACCAATTGGTTGGCTGAACAAAATGATACAAT------------------
upper sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G09130.2 (Glycine max), 3'ss of exon 5
------------gtctgcttcacatatttacattatatgatgatgtttgttgcaggtgcccttgtggagctgaatgttttatgttgttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
| |||| || | ||| | | | || | || || | || | | || || | | || ||| ||| |||||||||| ||||||||||||||||||| || || ||||| || ||||||||||| || ||||| | || || ||||||||||| |||| |||||| || |
gttctttgcaaattttgctccaaacctttttgggaaaatagtatttgtggtggaaatgtcaagatcaccgtggataaatgacatttgttt-tgtgcatacagGCTTCAGTATTTGTACAGTCTCATGTTCGGGCACATGTAGAATTGATGTGGCTGCTAAGTTCCACAACACCAATTGGTTGGCTGAACAAAATGATACAGT------------------
upper sequence: LOC_Os01g54020.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 5
gtctgcttcacatatttacattatatgatgatgtttgttgcaggtgcccttgtggagctgaatgttttatgttgttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
|| | || | |||| | | ||| || ||| | | || | || |||| | | | ||| | ||||| ||| | ||||| ||||||||||| ||||| ||| || ||||||||| | ||||||||| ||||||| ||||||||| | |||| |||||| || |
gtttagtttaactattcattctttattgtg--------tgccaaggtttatatgca--tgcttgttatgactcagatc-tgtatgggcagGCCTCTGTCTTTGTTCAGTCTCATGTTCGTGCCCATTCAGAATTGATGTGGTTACTGAGTTCTGCTACTCCAATTGGTTGGTTGAACAAAATGATTCAGT------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggagctgaatgttttatgttgttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
ttttatgttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgcttcacatatttacattatatgatgatgtttgttgcaggtgcccttgtggagctgaatgttttatgttgttttgtgtctttacaggcttctatatttgtacagTCTCATGTCCGTGCTCATGTTGAGTTGATGTGGCTTCTGAGTTCTTCTACTCCTATTGGTTGGCTCAACAGAATGATCCAATTCAAAGAGAAGTCACGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT