Sequence
atgc intronic sequence ATGC exonic sequence...cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g45410.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
----cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
||| ||| | | | ||| | | || ||| | ||| | || | || ||| || |||| || || | | || | | |||||||||||||||||| || |||||||||||||||||||| ||||| || || ||||||||||||||||||||||||
cattctttctttgttatg-attatat-aatgtagcaacctgatttttgctgtgttttctcagttatt-atatttt-gtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
-cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaat-ttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
|| || | | | | | | || | || | ||| || || || || | |||| |||| | | | | | | | |||||||||||||||||| || |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||||
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatct--tgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 3
cttagattgatttacactatgtcagtggcgcacta--tataatttcatactcatttgctgta-atttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
|| ||| | || || | | | || ||| || || || || ||| | | || | | | ||| || | | |||||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || |||
ttttatctgagat-caataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcactgctaatgtcta--tcatttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 2
cttagattgatttacactatgtcagtggcgcacta--tataatttcatactcatttgctgtaattt----atgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
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ttgctatctgaaatcaataattaatttgcatgctagatatgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatcttt-----gtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT-
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
cttagattgatttacactatgtcagtggcgcacta--tataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttca---taaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
|| ||| | || || | | | || ||| || || || || ||| | | |||||| | ||| | || ||| | | |||||||||||||| ||||| ||||| || || |||||||||||||| || || || |||||||| || || |||
ttttatctgagat-caataattaatttgcatgctagacatgtctttatgctgattgg---tcatttat-ctgcagtgcttatgtctatcttttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 3
-cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
||||| | | | ||| | | || | ||| | || | || ||| | | | || | | | || || | ||||||||||||||||| || ||||| || |||||||| || |||||||| | ||||| || || || ||||||
aattagaatctaagatattatctgtttttggcttttgctaaactaatttgccttagcta-agctcgtcttatgtaatacctcttgtgttttatgtttccagCGTTTTGCTGCGGTGATAATGAGGATCAGAGAACCGAAGACTACAGCATTAATATTCGCCTCAGGGAAAATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
| | || || | | | | | | | || | | ||||| || | || | ||| || | ||| | | |||||||||||||| || |||||||| ||||| || |||||||| || ||| |||||||||| || || || |||
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatt-tgctgtaatttatgttttagtttgctaattcctc-ctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
| || | | | | | | || | | || || ||| | | || ||| | ||| | | || || | || | | |||||||||||| || ||||| ||| ||||||| || |||||||| || || || || |||||||| |||||||||
--ttgaatatcgtcgagtttactattgatactattcatttgttgatatttttggtgttgttacctatttgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 2
cttagattgatttacactatgtcagtggcgcactatataatttcatactcat-ttgctgtaatttatgt-tttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
| ||| | | || | | | | ||||| | | || |||| | | | | | | | | | |||||||||||| || ||||||||| |||| || || || ||||| || ||||| || |||||||| |||||||||
--ctggttgtcatgaagacaacttgtactgtgtttctcaggctgatactgttgcttttgcttcttattcacccaatgcgttggtgggtattgttgttcacagCGTTTTGCAGCTGTTATCATGCGAATCAGGGAGCCTAAAACAACTGCTCTTATTTTTGCATCCGGTAAAATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ29072 (Selaginella moellendorffii), 3'ss of exon 2
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
| || | || ||| | | || ||||||| | ||| | || || |||||||||||||| || |||||| | ||||||||||| ||||| || ||||| || ||||| || || || |||
------------------------------------gtttgtttgtgttctttttttttctcttgtgttttatgacttgtctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
upper sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
| | | ||| | | | | ||| |||||| || | || ||| | || || |||||||||||||| || |||||| | ||||||||||| ||||| || ||||| || ||||| || || || |||
------------------------------gtttgtttgtgttcttttttttctcttgtt-tttatgacttgtctctct---ctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
tgctaat putative branch site (score: 2)
ctaattcctcctttc CT-rich tract
taatttatgttttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - -catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctaa