Sequence
atgc intronic sequence ATGC exonic sequencegttagctgtttctataatctctgggacatgctagttgactataatggcattatttttttcagatgatgactatatgccaaataccatgtataatacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g06350.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g06350.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G812228_T01 (Zea mays), 3'ss of exon 10
gttagctgtttctataatctctgggacatgctagttgactataatggcattatttttttcagatgatgactatatgccaaataccatgtataatacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA
||||| | |||| || || ||| || || || | || | || || || | || ||||| | | | || |||| ||| ||||||||||||| ||| |||| ||||| ||| | ||||| || ||||| ||||| ||||||||||| ||||| ||||| |||||||| |||||
gttagttatttccgcaacttc---aacac---agatgggggtattcatgagtttatcttggaataatcgttctaattaaaatagtct-tgtgatgcagGAGATATTGGCGAGTGGCAGCCAGATGGATCCTTAAAAGTGATTGATAGAAAGAAGAATATTTTCAAGCTTTCGCAGGGGGAATACGTTGCAGTGGAAAA
upper sequence: LOC_Os06g06350.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S218_19V6.1 (Physcomitrella patens), 3'ss of exon 16
----------------------------------------------gttagctgtttctataa---------tctctgggacatgctagttgactataatggcattat----ttttttcagatgatgactatatgccaaataccat-gtataa-tacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA
| ||| |||| | | | | || | | | ||| |||| | || | | | | || ||| | ||| || | | | | | ||| || | |||| ||| | || |||||| | | |||| |||||||| ||||| ||||||||||| || || |||||| | |||||||| ||||| ||||| || || ||
gtaatgtcttctctttaattgacgttttctttttaaataatttggatcttgctttttccctcagagagtgtctttttgtttcgttggaattgtttatattaacactgtggaactgctgcatatggt--ctacattctgattctcttcgtaaaactgcagGTGATATCGGGGAGTGGAAGAAAGATGGATCCTTGAAGATCATCGACAGGAAGAAGAACATCTTCAAGTTGTCACAGGGTGAATACGTTGCTGTCGAGAA
upper sequence: LOC_Os06g06350.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
gttagctgtttctat--aatctctgggacatgctagttgactataatggcattatttttttcagatgatg-actatatgccaaataccatgtataatacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA
|| | | | | | || | || || | | ||||| | | ||||| | | | | || ||| || | |||| ||| |||| |||||||| || |||| | |||| || |||||| | ||||| ||||| ||||||||||| |||||||||||| ||||||| |||||
gtcaccaatatacgtggaaaaaacgatgcagtttatgtaaacg-aatggtgctggaggagagcgctgatgtattctgattcttttataatgcatgaatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggcattatttttttcagatgatgactatatgccaaataccatgtataatacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA
attatttttttcagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctgtttctataatctctgggacatgctagttgactataatggcattatttttttcagatgatgactatatgccaaataccatgtataatacagGGGATGTTGGCGAGTGGCAACCAAATGGGTCCTTGAAAATCATTGACAGGAAGAAAAATATATTCAAGCTTTCACAGGGAGAATATGTTGCAGTAGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA