Sequence
atgc intronic sequence ATGC exonic sequence...gccctcaggaaacggagaaaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02150.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 2
gccctcaggaaacggagaaaattcct---gcgttccagaggctc--aaaccactgacaggaaatttaaacct-tactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
|| | | | | ||| ||||| | | | || | | || | || |||| | || |||||| |||| | ||||||||||| |||| || || ||||||||||| || |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||| || |
-----catgcagttgtagccctccctttaatgttcctgtaacccctaattcgtgggcactactttgcaaccaatgctataaatcat-gtgatttcttgtcttgcagGGCTTATCACCATACGAGAAGAAAAAATATGTATGGAAAATGCTTTACATTTATATGCTGGGTTATGATGTTGATTTTGGGCATATGGAAACTGTCTCGT
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 1
-gccctcaggaaacggagaaaattcctgcgttccagaggctcaaaccactgacaggaaatttaaacct--tactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
| | | | | ||||| || | | | | | | || | ||| | | | || |||||| ||||| | | |||||||||| | || || || ||||||||||| || |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||| || |
agttgtaggcttgtagccctcccttgaatgttcctgaaaccccta--aattatgggcactttgcaaccaatgctataaatcat-atgatttcctatcttgcagGGCTTGTCACCATACGAGAAGAAAAAATATGTATGGAAAATGCTTTACATTTATATGCTGGGTTATGATGTTGATTTTGGGCATATGGAAACTGTCTCGT
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 1
gccctcaggaaacggaga-----aaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatc--taccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
|| || | || | | |||| || || | | || || | | | || || | | | | | | | |||| ||| | | || |||||||| || || || || |||||||||||||||||||||||||| || |||||||| || ||||| ||||||||| ||||||||
------agaaattgatgatccatgattccctggattgcaatgtcaagaatttcttttattgactagtaaactaatatatcttttttacctttggttctatctt-tagGCTTTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGATATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 1
gccctcaggaaacggaga-----aaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
| | || | | ||| | || || | |||| | || ||| ||| | | ||| | | | |||| ||| || | || |||||||| || || || || |||||||||||||||||||||||||| || |||||||| || ||||| ||||||||| ||||||||
---ttgatgatccatggttccctggattgcaatgtcacaagaatttcttttgttgactagtaaactaatatttatttttttttacctttggtt-ctatctt-tagGCTCTGACTCCATATGAGAAAAAGAAATATGTTTGGAAAATGCTTTACATATATATGCTTGGCTATGATGTGGATTTTGGTCACATGGAAGCTGTTTCTC
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 1
gccctcaggaaacggagaaaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttg-cagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
| | | || | | || | | | | | | | | ||| || || || || | ||| ||||| | | || ||||| || || || || || ||||||||||||||||| |||||||||||||||||||| || ||||| ||||||||| | ||||||
-gcattattaacccatgttgatgtgcaggctgtctaattttttttatttatttcttcttctgtatcttcctttaacccaaaatttgatggtcctttgacagGGTTTGACACCATATGAAAAAAAGAAATATGTCTGGAAAATGCTTTACATTTATATGCTGGGTTATGATGTAGATTTTGGTCACATGGAAGCAGTTTCTC
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 1
---gccctcaggaaacggagaaaat-tcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
| | ||| | | | || || || || |||| ||| | | || || | || | || ||||| | || || |||||||| ||||| || ||||| ||||| ||||| || ||||| || |||||||| ||||| || ||||||||||| ||
tttttcttgaggtagcctgtatggcatcaaatgtcatggattgtcgaacccaagacttttcacacgcggtatgttgcaattt--tgccatttgtgttcc--cagGGCTTGTCTGTATACGAGAAGAAGAAGTATGTTTGGAAGATGCTATACATTTACATGCTTGGCTATGATGTGGACTTCGGACACATGGAAACAGTGCAAC
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 1
gccctcaggaaacggagaaaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttg--cagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
|| || | ||| || | | || || | | ||| ||| | |||||| | ||||||||||||||||||| ||||| ||||| ||||| ||||| | ||||| ||||||||||| || || ||||| |||||| | || ||||
----------------------------gtgagtgatctttttcttgctgcttgggtttcttcgtctcg-----gattgctaagattgcccgcttgcgccagGGATTGACGCCTTATGAGAAGAAAAAATACGTTTGGAAGATGCTCTACATCTTCATGCTTGGTTATGATGTCGATTTCGGGCATATGGAAGCGGTGTCTT
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ21842 (Selaginella moellendorffii), 3'ss of exon 1
gccctcaggaaacggagaaaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttg--cagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
|| || | ||| || | | || || | | ||| || | |||||| | ||||||||||||||||||| ||||| ||||| ||||| ||||| | ||||| ||||||||||| || || ||||| |||||| |||| ||||
----------------------------gtgagtgatctttttcttgctgcttgggtttcttcgtctcg-----gattgctaagattgctcgcttgcgccagGGATTGACGCCTTATGAGAAGAAAAAATACGTTTGGAAGATGCTCTACATCTTCATGCTTGGTTATGATGTCGATTTCGGGCATATGGAAGCTGTGTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
ccgtctt CT-rich tract
aaatttaaacctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccctcaggaaacggagaaaattcctgcgttccagaggctcaaaccactgacaggaaatttaaaccttactgaaaatcaccatgatctaccgtcttgcagGGACTATCGCCTTATGAGAAGAAAAAGTACGTATGGAAAATGCTTTACATATATATGCTGGGTTATGATGTTGACTTTGGGCACATGGAAACTGTTTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - -ggagaaaa
- - - - - - - - - - -ttcctgc
- - - - - - - - - - - - - - - - - - - - -aaaccac
- - - - - - - - - - - - - - - - - - - - - - - - - acaggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatc