Sequence
atgc intronic sequence ATGC exonic sequence...gtgaacataaagaactgtttacaggttctctgtttgctacttatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g11120.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G029055_T01 (Zea mays), 3'ss of exon 7
-gtgaacataaagaactgtttacaggttctctgtttgctacttatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
|||| | | | | | || | ||| ||||||| | |||| ||||||||||||||| ||||| ||| ||||||||||| || ||||||||||||||||||||||| ||| |||||||||||||||||||||| ||||||||| | |||||||| | || |||||||||| |||||||||||||
gagcaacaaatgcatgtagattcccagtcaccttttatgttttatctccgcaagtcgcttttatttcatgcaccaatgatttctattttgaaaa-ttctagGATGGCATGAAGATGGGAAAGTCACTAGGCAACACACTTGAACCAAAAGATCTGGTAGAAAGATTTGGTGCTGATGCTGTTAGGTATTTCTTCTTGCGGG
upper sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G23250.1 (Glycine max), 3'ss of exon 7
gtgaacataaagaactgtttacaggttctctgtttgctact-tatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
|| | || | || || ||| | | ||| || | | | | ||| |||||||||||||||||||||||||||||||| | ||||||||| ||||||||||| || ||| |||| || | |||||||||||| ||| |||| || | |||||| ||| | ||||| ||||||||| | | |
actaaatttggcaatttttgacttagcaaagttttataaatctatttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaa-tgttagGATGGAATGAAGATGGGCAAGTCACTAGGGAATATACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTCCTCAGAG
upper sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G43550.1 (Glycine max), 3'ss of exon 7
gtgaacataaagaactgtttacaggttctctgtttgcta-cttatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
|| | | ||| | | | | | ||| | | | | || | | | | ||| |||||||||||||||||||||||||||||||| | ||||||||||||||||||||| || ||| |||| || |||||||||||||| ||| |||| || | |||||| ||| | ||||| |||||||| | | |
atgggtcttaggaaaagctaggaaactaaatttttataaacctgtttcttatatttaatttcatttcatgcagcaatgctttttattttgaaaa-tgttagGATGGCATGAAGATGGGCAAGTCACTAGGGAATACACTTGAACCAAACGATTTGGTTAATAAATTTGGGACAGATGCAGTTAGATACTTCTTTGTCAGAG
upper sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 3'ss of exon 7
gtgaaca--taaagaactgtttacaggttctc---tgtttgctacttatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
|||| || ||| || | ||| || |||| ||||||||| | | ||||||||||||||||||||||||||||||| |||| ||||||||||| |||||||||||||||||||| || || |||||||||||||| ||| |||| | |||||||| || | || || ||||| ||| | |||
---aacaattatagacatgatagtgagttatcagctgttaatattttatctcatataccta-ttttatttcatgcagcaatgctttttatttttaaaa-ttttagGATGGAATGAAGATGGGAAAATCATTGGGGAATACACTTGAACCAAATGATTTGGTTCAAAGATTTGGCTCGGATGCAGTAAGATACTTTTTCCTTAGGG
upper sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ17733 (Selaginella moellendorffii), 3'ss of exon 7
gtgaacataaagaactgtttacaggttctctgtttgctacttatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
| || || |||| ||| | | || ||||| || || |||||||| ||||||||||||| || ||||||||||| | || ||| |||| ||||| ||||||||||| || ||||| || |||||||| || |
------------------------------------------gtatccatgggttcttttttttttttttgttga--ctcgttattgtgc---tttccagGATGGCTTGAAGATGGGAAAGTCTCTAGGCAACACAATCGAGCCACAGGAGCTGGTCTCGAGATTTGGAGTTGATTCTGTGAGATACTTCTTTCTGAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
aatgctttttattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaacataaagaactgtttacaggttctctgtttgctacttatctcatccagtcacttttatttcatgcagcaatgctttttattttgaaaaattttagGATGGCATGAAGATGGGAAAATCATTAGGCAACACACTTGAACCAAAGGATCTGGTAAACAGATTTGGAGTAGACTCTGTTAGGTACTTCTTCTTGCGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- gaacata
- - - - - - - - - - - - - - - - - tgctact
- - - - - - - - - - - - - - - - - - - - - - - catccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgc