Sequence
atgc intronic sequence ATGC exonic sequence...tattctactgcacattggtagactggccaaacgctattatatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g04110.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 2
tattctactgcaca-ttggtagactggccaaacgctat--tatatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
|| ||| || || ||| | | | | ||||| ||| | || | || |||||| |||| ||| || || |||| ||| |||||||| |||||||||||||||||||||||||| |||| ||| |||||||||||||||| |||||||||||||| |||||||||||||||||||| ||||||||
--tttagctgttcaattagtacctagcatatgtgaaagaatatatacattctacaag-gaaatatttggaatgcaataatttatgtctgctctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGTCACGTGAATAATGTGTCCTGTGTGATGTTCCATGCGAAGCAAGACATCATTGTGTCTAACTCAGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 2
tattctactgcaca-ttggtagactggccaaacgctatta----tatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
|| | | || || || ||| || | | | | ||| ||| | || | || | ||||||||| |||||| |||| | ||| |||||||| |||||||||||||||||||||||||| |||| ||||||||||||||||| || |||||||||||||| |||||||||||||| ||||| ||||||||
--tttagcagatcaattagt--acttagcatatgtgaaaaagagtatacattctacaag-gaaatgtttgaaatgcaataatctatatgtgttctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGCCACATGAATAATGTGTCTTGTGTGATGTTCCATGCGAAGCAAGACATCATCGTGTCAAACTCAGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 2
--tattctactgcacattggtag-actggccaaacgctattatatgca-taccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
| | | | || ||| | | |||| | || | | |||||| | | || | | | | || |||| ||||||||||||| |||||||| |||||| || | || |||||||||||||| || || || ||||||||||| || || |||||||||||||| || || ||
gcttgcatgcattaactttttagtatttagtaaaccaaaaaatgtttggtttttttattgaccttctcaaagtccctaatattttttcccctgtttt----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
----tattctactgcacattggtag-actggccaaacgctattatatgca-taccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
| | | | || ||| | | |||| || | | | || | ||| | | || | ||| || | | | |||| ||||||||||||| |||||||| |||||| || | || |||||||||||||| || || || ||||||||||| || || |||||||||||||| || || ||
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtc-cctaatatat-tttcccgtttt----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 2
--tattctactgcacattggtagactggccaaacgctattatatgcataccactattga-ggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
|| || || | | | || ||| | || | | || ||| || || | | | | | | | | | ||||||| ||||| |||||||| || || ||| | ||||||||||||||||| || || || ||||||||||| || || || ||||||||||| || || ||
taaatcttaagatgtat-accatgttttttggatgc-gttaaacttgtagtgtttgaggtggcattgtttttgctgttaatgatttat-ttctctattgtcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGATATCATTGTGTCAAATTCTGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 2
tattctactgcacattggtagactggccaaacgctatta-tatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
| | | | || || ||| || | || || || | ||||||| | ||| || | | ||| | | | | ||||||| ||||| |||||||| || || ||| | ||||||||||||||||| || || || ||||||||||| ||||| || ||||||||||| || || ||
ggatgcattaaatataaatattgtgggatgtggcgaataataagcttgtagtgtttgaggtgctgcttatgctgttaatgatttgta-tctctattttcagACACAAAGGCATGGGAAGTGGACACCTTGAGAGGGCACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAGCAGGATATCATTGTGTCAAATTCCGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
-tatt-ctactgcacattggtagactggc-caaacgctattatatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
|||| || || | || || || || | ||| | || | ||||||||| |||||| | || | || | |||| || || |||||||| || ||||| ||||| || || |||||||| || || | ||| |||||||||||||| || ||||| || ||||| ||||| ||
gtatttcttatggatatctgtcttcttcttcacagaaagttaattttatga-atcattgaggtac------tgatgcgtttcaattttgttg--------cagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 3
tattctactgcacattggtag-actggccaaacgcta---ttatatg-cataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
||| | || | | | | | | || ||||| | | | ||||| || | | ||||| || | | ||| ||| ||||||| |||||||||||||| ||||||||| ||||||||||||||||||| || || || | || ||||||| ||| || | |||||||| || |||||
-tttcatccatttgttaatcgtattttctttttgttagggttatagaactttgtagaattgaactagctaatggtttgcaacttaccttttctacttt----cagACACAAAGGCTTGGGAAGTAGATACTTTGAGGGGGCACATGAATAATGTTTCATGTGTCTTCTTTCATGCAAGGCAGGATGTGATTGTGTCAAATTCAGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ37162 (Selaginella moellendorffii), 3'ss of exon 2
tattctactgcacattggtagactggccaaacgctattatatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
| | | | | | | | ||| | | | | || | | ||| | || | |||||| ||||||||||| |||||||||||||| || |||| || || || ||||| || ||||||| || || |||||||| || || ||||| ||
----------------------------gtatgtgaacttcttcttttttttcttgtcatgctgtctagtttctaaac---gcttgcattggttctatagACACAAAGGCTTGGGAGGTTGATACTTTGCGCGGTCACACCAACAACGTTTCCTGTGTCCTGTTCCACGCTCGCCAGGACATCATCGTCTCTAACTCGGA
upper sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ08647 (Selaginella moellendorffii), 3'ss of exon 2
tattctactgcacattggtagactggccaaacgctattatatgcataccactattgaggtatttgaaatgatgcaa----tctaagtg--tgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
||| || | | | || | ||| ||| || ||||| | ||| | || | |||||| ||||||||||| |||||||||||||| || |||| || || || ||||| || ||||||| || || |||||||| || || ||||| ||
------------------------------------gtatgtgaacttcttttttttttttcttgtcatgctgtctagtttctaaacgcttgcattggttctatagACACAAAGGCTTGGGAGGTTGATACTTTGCGCGGTCACACCAACAACGTTTCCTGTGTCCTGTTCCACGCTCGCCAGGACATCATCGTCTCTAACTCGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
ctattttt CT-rich tract
tatttgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattctactgcacattggtagactggccaaacgctattatatgcataccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA