Sequence
atgc intronic sequence ATGC exonic sequenceTGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g21160.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
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TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgc----attgcgttgcgaattcatcctt-cgcttccagcaacggcaatggcgtccgtgca----tgcacgcatgcagttgcttgggttaactgatctgct-gttctcgcctcgcag-------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G819035_T01 (Zea mays), 5'ss of exon 4
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacg--ttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| ||| |||||||||||||||||||||||||||||||| | ||||||||||||||||| |||||||||||||||||||||||||| ||||||||| | | || || | | | || ||| || || || | || || | ||| | | | |||| || || ||
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACACACGCGTGCTCGTCAAGCCGTACAAGGAGAAGGGCAAGGTCCCCGATAAGTACAGgcatgcattgcgaattcatcct---tggcttccagcaacggcaatggcgtccgtgcatgcacatatgcagttgctcgggttaattgatctgctgttctcggct--------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G086614_T01 (Zea mays), 5'ss of exon 3
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| ||| |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||| | | | | | || || | ||| ||| | | | | | ||| | || || | ||| | |||| | | | |||
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTGCAGgcatgcactgcgagttcatcctttgcttgctcccagcgaccgcaatggcggccgccctacgtgcat-gcagt-------tgctccggggattgactgatttgct-gttctcgctccgcag-------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G819035_T02 (Zea mays), 5'ss of exon 4
-----------------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| ||| |||||||||||||||||||||||||||||||| | ||||||||||||||||| |||||||||||||||||||||||||| ||||||||| | | | ||| || | | | || || ||| || | || | | ||| | || ||| |||
CGTCTATCCAGAGACCGTGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACACACGCGTGCTCGTCAAGCCGTACAAGGAGAAGGGCAAGgtccccgataagtacaggcatgc----attgcgaattcatccttggcttccagcaacggcaatggcgtccgtgc---atgcacatatgcagt-tgct--cgggttaattg----------------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G086614_T02 (Zea mays), 5'ss of exon 3
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
|| |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||| | | | | | || || | ||| ||| | | | | | ||| | || || | ||| | |||| | | | |||
---------TCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTGCAGGCATGCACTgcgagttcatcctttgcttgctcccagcgaccgcaatggcggccgccctacgtgcat-gcagt-------tgctccggggattgactgatttgct-gttctcgctccgcag-------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G01350.1 (Glycine max), 5'ss of exon 3
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
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TGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcaccccctcttt-ctactcttatgttaactttt-----tgtttttgttattccctt-gagtttgttttg--aatgtgct-cactattgtttcttgtgatttgcag---------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA11G01780.1 (Glycine max), 5'ss of exon 3
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||| || || || |||| || || || || || ||||| || | || || || ||||||||||||||||||||||| || ||||| |||||||| | | | | | || ||| | || | ||| | ||| || | | || | || || |
AGACAGTGAGACTCATATTATCCAAAGGGAATCCTCATTTTATCTGTGATTCACGTGTACTTGTCAAGCCCTACAAGGAGAAGGGAAAAGTCCCTGACAAgtaagtatgcat------catgtttttaattgg----tttatatcttactat--------tcctaaactaatgtgactaatttattatgcag-----------------------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G01350.2 (Glycine max), 5'ss of exon 3
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| || | | || || ||||| || || | || || || || ||||| || ||||| ||||||||||||||||| ||||| |||||||||||| || | | || ||| | | | || ||||| | || | || || | | | | || | ||| || | || | ||
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccctcttt-ctactcttatgttaactttt-----tgtttttgttattccctt-gagtttgttttg--aatgtgct-cactattgtttcttgtgatttgcag---------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G43700.1 (Glycine max), 5'ss of exon 3
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||| || || || |||| || || || || || ||||| || | || || || ||||||||||||||||||||||| || ||||| |||||||| | | | | | || | || | | | ||| ||| | ||| || || || | || |||| | ||
AGACAGTGAGACTCATATTATCCAAAGGGAATCCTCATTTTATCTGTGATTCACGTGTACTTGTCAAGCCCTACAAGGAGAAGGGAAAAGTCCCTGACAAgtaagtatgcat------catgttttaattg-------gtttctg----tatcttactattcctaaactaatactatt-gtg-actaatttattatgcag---------------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA12G01340.1 (Glycine max), 5'ss of exon 4
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| || | | || || ||||| || || | || || || || ||||| || ||||| ||||||||||||||||| ||||| |||||||||||| || | | || ||| | | | || ||||| | || | || || | | | | || | ||| || | || | ||
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccctcttt-ctactcttatgttatcttttttttgt--ttttgttattccctt-gagtttgttttg--aatgtgct-cactattgtttcttgtgatttgcag---------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G35990.1 (Glycine max), 5'ss of exon 7
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccacca--acctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| || | |||| || || || || || | || || || || ||||| || ||||| ||||||||||||||||| ||||| |||||||||||| || | | | | | | | || || | | || || | || | | || ||| |||| | || | | ||||
TGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcac--ccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtt--tattttgaatgtcctcattgatgtttcttgtgatttgcag-------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G35980.1 (Glycine max), 5'ss of exon 4
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccacca--acctgcatgcatgtgaatttgttgttcgtcgctcctcag
||||||| || | |||| || || || || || | || || || || ||||| || ||||| ||||||||||||||||| ||||| |||||||||||| || | | | | | | | || || | | || || | || | | || ||| |||| | || | | ||||
AGACTGTGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcac--ccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtt--tattttgaatgtcctcattgatgtttcttgtgatttgcag-------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 5'ss of exon 3
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
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AGACTGTGAAGAGCATTCTGGCCAAAGGGAACCCTCACTTTGTGTGTCATTCCAGGGTTCTTGTTAAGCCTTACAAGGAGAAAGGCAAAGTCCCAGACAAgtacaggtactttggcttttcctccttgagctgctcctgattcctcatctctttacgacgctttgattcctctgctgcag-----------------------------------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G51950.1 (Arabidopsis thaliana), 5'ss of exon 5
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
| ||| || | ||||| || || || ||||| | || || || | || || |||||||| ||||||||||| ||||| ||||| ||||| ||||||||| | | ||| | || | || | | | | || | | | ||| | | | | || | |||| || | |||| | | |
TTAAGAGCATTCTCGCCAAAGGGAATCCTCACTTTGTGTGTGATTCCAGAGTTCTTGTCAAGCCTTACAAGGAGAAAGGCAAAGTCCCTGACAAATACAGgtactt-----atattgctagtattagtaact-cttatact-ttggcctgattgttcc----ttgaatcccttgtgt-ttactgcg--gtttgttgtg-cag-------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G63450.3 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
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TGAAGAGCATTCTGGCCAAAGGGAACCCTCACTTTGTGTGTCATTCCAGGGTTCTTGTTAAGCCTTACAAGGAGAAAGGCAAAGTCCCAGACAAGTACAGgtactttggcttttcctccttgagctgctcctgattcctcatctctttacgacgctttgattcctctgctgcag-----------------------------------------------------------------------------
upper sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 5'ss of exon 4
------TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattag-tagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
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AGACAGTGAAGCTCATTTTGGCTAAAGGGAACCCTCATTTTGTTTGTGATGCTCGGGTTCTGGTTAAGCCCTATAAGGAGAAGGGCAAAGTCCCGGACAAgtacaggcactctc----ttctgctctccctct-aaatgccttggtttttttggtgcatcttgcagagtagctgatggtaatttttggtttcag----------------------------------------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|163928946|gb|EG711958.1|EG711958EST: GTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG GAAGCAGCAGCAAGGCGATTTCTGCTGCATGTCGCCCACGGGGTTAGACGC
genomic: GTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcga ... cgctcctcagGAAGCAGCAGCAAGGCGATTTCTGCTGCATGTCGCCCACGGGGTTAGACGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA