Sequence
atgc intronic sequence ATGC exonic sequence...gcatcatgttttttttttccacaataattgcctttttttgggtcaaatattcttcaacccataaatgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g47520.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g47520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G142664_T01 (Zea mays), 3'ss of exon 4
-gcatcatgttttttttttccacaataattgcctttttttgggtcaaatattcttcaacccataaatgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
|| ||| ||| |||| | || ||| | ||| | | | |||| ||| |||||| || ||| || ||||||| || ||| ||||||||||||||||||||||||||||| || ||||||||||||||||||||||| || ||||| | ||||||||||||||||||| ||
tccaacatcatttattttaaaatgatgatttgccgatttatcttgagtcaatctttcaccaataaataacggg-aaattctggtacttatctgatttccagATCATAGATGCTGTTGTTGCAGCCCGCATACTGAATGCAACACTTGTCATTCCAAAGCTGGACGAAGAATCCTTCTGGAAAGATGCGAG
upper sequence: LOC_Os04g47520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G20550.1 (Arabidopsis thaliana), 3'ss of exon 4
gcatcatgttttttttttccacaataattgcctttttttgggtcaaatattcttcaacccataaa-tgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
| ||| ||| | | || | | | | | || | | | | ||| | ||| | | || | ||| | |||||||| |||||||||||||||| || | ||||| || || || ||||| ||||| || |||| |||||||||| |||||||||||| ||
---gtaagttcctttaggtttctctggttttatggtgatctttttgttgttacttagatcttggtctgagtttcaca--acgc-aattactt--ctttcagATTGTAGATGCTGTTGTTGCTGCAAGGATTCTAAACGCTACGCTTGTTATTCCGAAGTTGGACCAGAAATCCTACTGGAAAGATGCCAG
upper sequence: LOC_Os04g47520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv03s0038g03240.t01 (Vitis vinifera), 3'ss of exon 4
--gcatcatgttttttttttccacaataattgcctttttttgggtcaaatattcttcaacccataaatgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
| | | || ||||| ||| | ||| | || | | | | | || | | || || | | ||||| | |||||| ||||||||||| |||||| ||||||| || ||||| ||||||| |||| |||||||| || ||||| ||| ||
acatacttcactcatcattagaacaatgtggaggtttataatggttg--tgttactaatttagttttttatcctgagtatgttatatccatcatggctgcagATAACAGATGCAGTTGTTGCAGCTCGTATTTTGAATGCCACTCTTGTTGTTCCCAAGTTGGACCAGAAATCTTTTTGGAAGGATAGCAG
upper sequence: LOC_Os04g47520.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 3'ss of exon 4
----gcatcatgttttttttttccacaataattgcctttttttgggtcaaatattcttcaacccataaatgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
| | || || |||| | || || | |||| ||| |||| || || | | | || || || ||| || ||||||||| | ||||||||||| || ||||| ||| | ||||| || |||||| |||| || ||||||||||| ||||| |||| ||||| ||
actatggtgctattgttgttttaccttttagttacagaattttttatca--tattattaaatttgttgctcaggct--gagcttgttacacctgccattttcagATAACTGATGCTGTTGTCGCTGCCCGCATTTTAAATGCTACTCTTGTCGTTCCAAAACTGGATCAGAAGTCCTTTTGGAGGGATGCTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattcttcaacccataaatgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
ttttc CT-rich tract
ataaatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatcatgttttttttttccacaataattgcctttttttgggtcaaatattcttcaacccataaatgactctcaaagaatgctacttatgtggttttcagATCATAGATGCTGTTGTTGCAGCCCGTATTCTGAATGCAACACTTGTCATTCCCAACCTGGATCAGAAATCCTTCTGGAAAGATGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG