Sequence
atgc intronic sequence ATGC exonic sequenceTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccctttgtggaatattcatttttcattatcctgttggtgcttaaactaaatcattttttcttgatttccttgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 14
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccc--tttgtgg------aatattcatttttcattatcctgttgg---tgcttaaacta-aatcattttttc--ttgatttccttgtag------
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TGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGATTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCTAGATCTGAGgtaatactattttgtggtccttcagtaatgaatattaaaaattttatttgaattgctgaatttttaatcgtctgtgtggttgatctattggtcttatatt
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 11
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccctttgtggaata-ttcatttttcattatcctgttggtgcttaaactaaatcattttttcttgatttccttgtag--------------------
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TGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGGTTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCGAGATCTGAGgtaatactattttgtggtccttcagtaatggttattaaattt-tatttgagttactgagtttttaatcttctgtgtggttgatctattggtcttatgttta
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 11
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccctttgtggaatattcatttttcattatcctgttggtgcttaaactaaatcattttttcttgatttcctt-gtag------------------------
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TGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAGgtgatattattttctagtgctaatgtaatatttgtcaacttttatttgatccactggattttttttttacctcttttgtttgatttaatgatcttttgtttgcag
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 13
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 5'ss of exon 14
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccctttgtggaatattcatttttcattat------cctgttggtgctt----aaactaaatcattttttcttgatttccttgtag
||| ||| | || || ||||||||||||||| | |||||||| ||||| ||||| | || |||||||||| |||||||| ||||| |||||||||||||| ||| ||| | | || || | | | ||| | || || | || | ||||||| || || || ||
TGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAGgtgagaggcttg-ggattttccaccttcaactttgccccgcctatagggattttctgataccgtgt-attttttttttccttttttacag
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 14
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgta------tcccctttgtggaatattcatttttcattatcctgttgg---tgcttaaactaaatcattttttcttgatttccttgtag
||||||| | || || ||||||||||||||| | |||||||| ||||||||||| | || | |||||||| ||||||||||||||||||||||||||||| || | | | | | | || || || || | |||||| ||| ||| ||| || ||| ||
TGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAGgtgagaggctcaagtctttatatcttcaagttcagcttgtcttgattaatttgcttatactgtgtcaatttctccc----cttttgcag
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 13
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgta------tcccctttgtggaatattcatttt---tcattatcctgttggtgct-taaactaaatcattttttctt----gatttccttgtag----------------
||| ||| |||| || || ||||| |||||||||||||| || ||||| || || ||||||||||||| ||||||||||| || | ||| ||| ||||||| | ||||| | | ||||||| | ||| | ||| | | | | || | || || || | | |||| |
TGGTGATAGGACTCCCAAACAGAAGGTGAAATTGAAAGTCACAGAGGAGAAGCTATTGAATTTGATGTTAAAATACAATGGGGGGAGGCCTAGATCTGAGgtgcttactttcccttcatctttttctcattttgttttattgtattgtcaatattcttatttatgtaatcgcttattagatggtgcatttgttgatgatctcttttgcagMapped 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|29674285|gb|CB670560.1|CB670560EST: AACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG ACAAAACTGAAAAGTGCCGTGCAACTACAAGACTTGCTAGATGCCACAAGG
genomic: AACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccctt ... ttccttgtagACAAAACTGAAAAGTGCCGTGCAACTACAAGACTTGCTAGATGCCACAAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAGgtatcccctttgtggaatattcatttttcattatcctgttggtgcttaaactaaatcattttttcttgatttccttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA