Sequence
atgc intronic sequence ATGC exonic sequencegtaattccttatcctgcttggccagtgttttagctctgggcctgtgagcatctccctgtatcaagcatgccttttgtcatctagGTGCGAATGGAAACTCCATCTGGTATAAAGGATTCTATTCCTGCCTGGATCAAGTACTCTGTGCAGGCCGCAGGAGAAATCCCATACAATGGAATATATT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32660.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 7
gtaattccttatcctgcttggccagtgttttagctctgggcctgtgagcatctccctgtatcaagcatgccttttgtc---atctagGTGCGAATGGAAACTCCATCTGGTATAAAGGATTCTATTCCTGCCTGGATCAAGTACTCTGTGCAGGCCGCAGGAGAAATCCCATACAATGGAATATATT
||| ||| ||| |||| |||||| ||||| |||||||||| | | || ||||| | || |||||| ||||||| |||||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||| |||||||||| ||||| |||| || ||||
gtagccgctttacctcattggttgttgttttt-tgctggg-----gagcatctccaaaattaactggtgtgttttgaccatatatagGTGAGAATGGATACTCCATCAGGGATAAAGGATTCAATTCCAGCCTGGATCAAGTACTCAGTGCAGGCCCCAGGAGAAATACCATATGATGGGATTTATT
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 7
----gtaattccttatcctgcttggccagtgttttagctctgggcctgtgagcatctccc----tgt--atcaagca-tgccttttgt-ca----tctagGTGCGAATGGAAACTCCATCTGGTATAAAGGATTCTATTCCTGCCTGGATCAAGTACTCTGTGCAGGCCGCAGGAGAAATCCCATACAATGGAATATATT
| | | | | || ||| ||| | | || | |||| || | || || ||| | | ||| || || || || | || ||||| ||||||||||| || || || || |||||||| |||||||||| ||| ||||| || |||| |||||||||| |||||| ||||| |
tgtggataatattgctatgagttacacagatatttggttagaagcttctgagaatattatgtaatgacgatgaagtaatttcttatgcacaaaactccagATTCGTATGGATACTCCATCTGGCATTAAAGACTCAATTCCTGCTTGGATCAAGTTCTCGGTGCAAGCTCCAGGTGAAATCCCATTCAATGGCATATACT
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 7
-----gtaattccttatc-ctgcttggccagtgttttagctctgggcctgtgagcatctcc-ctgtatcaagcatgccttt--------tgtcatc-tagGTGCGAATGGAAACTCCATCTGGTATAAAGGATTCTATTCCTGCCTGGATCAAGTACTCTGTGCAGGCCGCAGGAGAAATCCCATACAATGGAATATATT
||| ||||| || || | | | | | ||| || ||| ||| | |||| ||| || ||| | | ||||| ||||||||||| || || |||||||||||||| |||||| ||| |||||| ||||| | || ||||| ||||||||||| |||||||
tatttctaaatccttgcaattgtttactttgccctaaaagctaagattcgagagggcctgtactgctgcaaataactctttataaacattgtgattgtagATCCACATGGATACTCCATCTGGCATTAAAGATTCTATTCCTGCTTGGATCGAGTTCTCTGTACAGGCTCCCGGTGAAATTCCATACAATGGTATATATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagctctgggcctgtgagcatctccctgtatcaagcatgccttttgtcatctagGTGCGAATGGAAACTCCATCTGGTATAAAGGATTCTATTCCTGCCTGGATCAAGTACTCTGTGCAGGCCGCAGGAGAAATCCCATACAATGGAATATATT
ccttttgtc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccttatcctgcttggccagtgttttagctctgggcctgtgagcatctccctgtatcaagcatgccttttgtcatctagGTGCGAATGGAAACTCCATCTGGTATAAAGGATTCTATTCCTGCCTGGATCAAGTACTCTGTGCAGGCCGCAGGAGAAATCCCATACAATGGAATATATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA