Sequence
atgc intronic sequence ATGC exonic sequenceGAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g20420.3 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30470.1 (Glycine max), 5'ss of exon 7
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattat-tgtag
|| || | ||||||| |||||| |||||||||| |||||| ||||||||||| |||||||| ||||| ||| | || | ||||||| ||||||||||||| | | | || | | || | | | |||| | || ||| | | || || ||| | | |||||
GAAAGATAGAGTTGGACCCTGGGAACAGAGACCTGGGCACTTTGGTGATGTTTGGAGCTATTGGACAGATGAAGGATTTGGTTATTTTGAGGGTCTTCAAgtaagtaca----tttattatga-taacaatcacattttgttg--ttattgtgaaattcaatcat---gacaagccattttttttttgtgtgtgtag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G27490.1 (Glycine max), 5'ss of exon 7
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
|| || | ||||||| |||||||||||||||||||||||| ||||||||||| ||||||||| ||||| ||| | || | ||||||| |||||||||||| | | | || | | || | | | |||| | || ||| ||| | | ||| | |||||
GAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTGGAGTTATTGGACAGATGAAGGATTTGGTTATTTTGAGGGTCTTCAAgtaagtcca----tttattatga-taacaatcacattttgttg--ttattgtgaaattcaatcat------aataagccattttttgtgtgtgtag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30150.1 (Glycine max), 5'ss of exon 8
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
|| || || ||||||| |||||||||||||| || |||||||||||||| ||||||||||||||||| |||||| | || ||||||||| ||| |||||| || || | |||| | | ||| || | | || || || || | |||||| | || ||
GAAAGACACGGTTGGACCCTGGGAAGAGAGACCAGGGCACTTTAATGATGTATGGAATTATTGGACTGACGATGGATTTGGTTTTTTTGAGGGCCTCCAAgtaggttttcctttcatatcagtaaataaactcatgggtatttaatttttcc--tattgaattgaaaaacttattc-ttctgtttc--tcgtgcag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30450.1 (Glycine max), 5'ss of exon 8
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagta---------aaatgctccagctt-ggctcagaac---tgaaagcagccaaataattgca--tcaacta-accattaagctgatacacgttgtttcattattgtag-----------
|| | |||||||||| ||||| ||||||||||| |||||| ||||||||||| || ||||||||||||||||| || | || |||||| || ||||||||| | || | ||||| || | | | | | || | ||| | | | | ||| | | | | ||||| | | || |||||| ||
GAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGTTATTATGAGTTTCTCCAAgtaagtgcctctttacatatattgtagcttaggattatgatgttcgtatctagtcgaattactctagttgtgctatgctagtgaaatgatatatataatt--attattataatttttgagcag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G00630.1 (Glycine max), 5'ss of exon 7
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaact-aaccattaagctgatacacgttgtttcattattgtag
|| || || ||||||| |||||||||||||| || |||| | ||||| ||||||||||||| |||||| ||| | || || |||||| |||||||||| | | | | |||| | | | ||||| | | || || ||| | ||||||| | | ||
GAAAGACACAGTTGGACCATGGGAAGAGAGACCAGGACACTATGGAGATGTATGGAATTATTGGAGTGATGACGGATTTGGTTTCTTTGAGGGCCTTCAAgtagg---gtttccttttataaactcatg--catatatggatatttaatttttcttattgaattgagaaatcgatctat-ttgtttctcga--gcag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 8
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagct----tggctcagaactgaaa-gcagccaaataattgcatca------------acta-accattaagctgatacacgttgtt-tcattattgtag--------
|| | | | ||||||| ||||| ||||||||||| |||||| ||||||||||| || ||||||||||||||||| |||| || |||||| || ||||||||| | || | | ||| || | | | | | || ||| || | ||| | | | | ||||| | || || | |||||| |
GAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGCTATTATGAGTTTCTCCAAgtaagtgcctcttttcatatattgtagctgaggaatatgatgttcatatctagttgaattactcttgttttgtgctatgctagtgaaatgatatatattattattattattatttttgagcag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G30460.1 (Glycine max), 5'ss of exon 7
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
|| || || |||||||| ||||| ||||||||||| ||| || |||||||||||| ||||||| |||||||||| | || |||||||||| || | || |||| | | || || | | | || | || ||||| | | | | | | ||| |||
GAAAGATACTATTGGACCATGGGAGGAGAGACCTGGGCACCTTGGTGATGTTTGGAACTATTGGAGTGATGATGGAATTGGTTTTTTTGAGTATCTCCTGgtgagtattcttttacaactataattaaatttgtc--ctgctgaataaatataata---------tgatttaatatttcttgagcag---------
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
|| |||||| | || ||||||||||||||||||| || | | |||||||||||| || |||||||||||||| || ||| ||||| ||| |||||||||| | | | | | || || | | || || | || |||| ||| | |||||| | | |||| ||||||
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttc-----tatatccatttaa---agtgtttcaa-taattactaagctcgaaacaaatatttc----ttgtag
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 5'ss of exon 8
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
|| |||||| | |||||||||||||||||||| || || ||| |||||||||||| |||||||| |||||||| || ||| ||||||||| ||||||| || | | || | | | || || || | || | | | | | | ||||| || || || || ||
GAAAGAAACCGTAGGACCTTGGGAAGAGAGACCGGGCCATTTTGGTGATGTTTGGAAGTATTGGACCGATGATGGCCTTGGCCACTTTGAGTTCTTTCAAgtgag---acttcttcttttctattgagtacataatgatccccgaagctcgt---tattgaatattaa----atgaacattcttgcag--------
upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 9
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaa----ctgaaagcagccaaataattgcatcaacta--------accattaagctgatacacgt-tgtttcattattgtag
|| | || ||||| || ||||| ||||||||||| |||||| |||||||||||| || ||||||||||||||||| || | ||||||||||||||||||| ||| | | || | || | | | | | |||| | | | | | || | || || ||||| || |||||
GAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGGAAGTACTGGACTGATGATGGACTTGGTTATTTTGAGTTCCTTCAAgtatgtatcttccacctgtcaattgtgaaagattttatttatatcttagtgattgtacaatttccatgagatgctgcttaggtaatttacaaatgttttgtttctgtagMapped 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|157650374|gb|EX450008.1|EX450008EST: TTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAA TTGGCAGAAGACCTTGATGCCTGCCCAGTTTGGGTGATCAATGATG
genomic: TTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaa ... attattgtagTTGGCAGAAGACCTTGATGCCTGCCCAGTTTGGGTGATCAATGATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag
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