Sequence
atgc intronic sequence ATGC exonic sequencegttgccactcatgcattggttgattagtaacaaatcgaagacctgatcaaacacacattgattaatccaaaaatggccttttatttgatttcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g23130.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g23130.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgccactcatgcattggttgattagtaacaaatcgaagacctgatcaaacacacattgattaatccaaaaatggccttttatttgatt-tcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
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----------------gtatgtatacacaatatacaatataattcaaaaattacatagtttttgtttgtaaca-gttacattatttatctgtcatgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
upper sequence: LOC_Os08g23130.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G55930.1 (Arabidopsis thaliana), 3'ss of exon 2
gttgccactcatgcattggttgattag-taacaaatcgaagacctgatcaa-acacacattgattaatccaaaa-----atggccttttatttgatttcat--acagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
| | | || ||| || | | | | | ||| | || | | | || | || | | | | || | ||||| | |||||| | || ||||||||||| ||| | |||||||||| ||| || || ||| | || ||||||||||||||||| | || |||||| | ||||| ||
-------tgtgggtaatagtcatttaaatactagaactatggcctaagaaacaaatatttttaacgatttgtgatctttaagactttaacaatcatttcttttgcagTTGTTGGGATATGGATGGGCTGGAATCTTCAGGAAGTTCCTTGTGGATTCACCGTATATGTGGTGGCCGTCAAATTTGGTTCAAGTCTCACTCTTTAG
upper sequence: LOC_Os08g23130.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0015g00860.t01 (Vitis vinifera), 3'ss of exon 2
gttgccactcatgcattggttg-attagtaacaaatcgaa-gacctgatcaaaca--cacattgattaatccaaaaatggccttttatttgatttcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
|| ||| || | | || ||| | | | | |||| | | | || | | | | || || || ||| || ||||||||||| ||||||||||| || ||||||| || ||||| || ||||| |||| ||||||||||| ||||| || ||||||||| | ||||||||
--tgtagtatatggtttactcatactactaatccaccaattaatttgatattttagtttctcttgttcaccttgatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
upper sequence: LOC_Os08g23130.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
----gttgccactcatgcattggttgattagtaacaaatcgaagacctgatcaaacacacattgattaatccaaaaatggccttttatttgatttcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
|| | | || | | || || || ||| | | | || ||| || | | | | || || || ||| || ||||||||||| ||||||||||| || ||||||| || ||||| || ||||| |||| ||||||||||| ||||| || ||||||||| | ||||||||
atatattacttattttgtagtatatggttt-ccaccaattaatttgatattttaatttctcttg-ttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcaaacacacattgattaatccaaaaatggccttttatttgatttcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
ttttatttgatttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgccactcatgcattggttgattagtaacaaatcgaagacctgatcaaacacacattgattaatccaaaaatggccttttatttgatttcatacagTTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG