Sequence
atgc intronic sequence ATGC exonic sequencegtaagacactacgacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgatttggtttatgtgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67220.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 6
gtaagacactac-gacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgattt-----ggtttatgtgagtttcttactgtcaaa-atatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
||||| |||| | | |||||||| | |||| ||||||| ||||| | | || | | ||| | | || ||| || | ||| | | |||| ||||| |||||| |||||||| |||||| ||||||||| || | ||| |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||| | |||
gtaagtcactgcaggcatctttagtgtgcagtatgattaccaaagttttcttgacgcttaaacggatgatt-acatatgagattcttttcgagacaattt-tttatccagaagtggttgcaa-cttgattttctgtagtttatatgagtttctcaccataaaacatatcccagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGGGTAAAGCATTGGATAACGATCAATGAACCTCTCCAAACTGCAATCAAT
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AC155376.2_FGT005 (Zea mays), 3'ss of exon 6
gtaagacactac-gacatctttactttgcactatgatttaa--------aaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaa-gtgcttgcaaacttgatttg--gtttatgtgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
||||| |||| | | |||||| | || | ||||| | | |||| | | |||| || || | || | | || ||| || | | | ||| || ||| ||| ||||| ||||||||| |||| | |||||||| || | ||||||||| ||||||||||||||| |||||||||||||||||||||||||||| ||||| |||||||||| |||||||||||||||||| ||||| ||||| ||| | ||
gtaagccactgcaggcatcttaagcgtgtagtatgaatgtatgattaccgaagttttcttaacacgcaaatgaatggtt-acatatgagattcttctcgactcaacctttttgtttcaaaagtgtttgcag-cttgatttgctgtttttacgagtttctcaccataaaaatatcctagGGAGTACTTTGCATTGTATGCAGAAGCTTGCTTTGCAAATTTCGGAGATAGAGTAAAGCGTTGGATAACAATCAATGAACCTCTCCAAACCGCAATCAAC
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 6
gtaagacactacgacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgatttggtttatg-tgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
|| | ||| | || | || ||||||||||||||| ||||| | || ||| || || | ||| || | |||| | ||| |||| |||| ||||||||||| | |||||||| |||||||||||| |||||| || ||||| ||| | ||||| || || |||||||| |||||||||||||| |||
--------------------------------------------------------ccttgtaa--atttgtttcctagtacctttattaagatgagtg---tagtt----gatttttcaatattctattattgaatggtgtggttctga-tgt-ggcatatgccagAGAGTACTTTGCTGTTTATGCAGATACTTGCTTTGCAAGTTTTGGGGATAGAGTGAAGAACTGGATTACTATTAATGAGCCCCTTCAAACTGCAGTCAAT
upper sequence: LOC_Os01g67220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 3'ss of exon 5
gtaagacactacgacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgatttggtttatgtgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
|||||| || || | ||| | | | | ||| ||| | ||| || | | || | || |||||| ||| | || ||| || ||| | || |||||| | ||||| ||| |||||||||||| |||||| || ||||||||| | ||||| ||| | |||||||||||||||||||| || |||
----------------------------------------------ttttaaa-----atttatctttgctattccaaacctcacatactggttgaaggatcca--ttattgttcatacataaatg-tttggtatattttggt------------aaacattgcagAAAATATTTTGCAATTTATGCGGAAACTTGCTTTGCAAGTTTTGGTGATAGAGTAAAGAACTGGATCACATTAAATGAGCCTCTTCAAACTGCGGTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcttgcaaacttgatttggtttatgtgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
ttcttac putative branch site (score: 2)
tcaaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacactacgacatctttactttgcactatgatttaaaaagtcatttaaacagccatataaccaatttataagggatattattattaagatgagtgatttagtttaaagtgcttgcaaacttgatttggtttatgtgagtttcttactgtcaaaatatcccagGGAGTACTTTGCACTGTATGCAGAAGCTTGCTTTGCAAATTTTGGAGACAGAGTAAAGCATTGGATAACAATCAATGAGCCTCTTCAAACTGCAGTTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG