Sequence
atgc intronic sequence ATGC exonic sequenceCTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagttctaccattttatgttgcttgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04660.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G174343_T07 (Zea mays), 5'ss of exon 2
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagttctaccattttatgttgcttgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag
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CGCTGTGCTGATAACTGCAGTTTTTACCGATGTGATAAAGACTGCAGTAGGGAGACCGAGGCCAGACTTCTTCTGGCGATGCTTTCCTGATGGAAAGCAGgtatacttccttgtatacatttgcgtgtagataattcttcc--ctagagatgctt----tttcatagttt--aaatcaacacagtgcttctatggtatatttggtgcag
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G53100.1 (Glycine max), 5'ss of exon 4
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagt-tctaccattttatgttgcttgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag
||| || | ||||| ||||| | ||| | |||| ||||||||||| ||||| | ||||||||||| ||||| |||||||| ||||||||| | ||| ||| | | || | | | ||| | | | || || || |||||| || ||| | || | | | | || || | || ||
CTCCGTTTTAATAACAGCAGTATTTACTGAGGCAATAAAAAATGCAGTAGGTCGACCTCGACCAGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgtatgttttcctttaattttaggttttcaattcatatttatcaatt-atgttggttcttaatagtgggcataattaattattagtggct-tcttgttag-----------
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G09820.1 (Glycine max), 5'ss of exon 4
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagttctaccattttatgttgcttgttatttgtcaattttga-aactgacaaggcactgttctggtaattttatctcag
||| | | ||||| |||| | ||| | |||| ||||||||||| ||||| | || |||||||| ||||| |||||||| ||||||||| | ||| | | | | |||| | || || || | || | || | |||| | | | || || | | | | ||||
CTCCATTTTAATAACCTCAGTATTTACTGAAGCCATAAAAAATGCAGTAGGTCGACCTCGTCCGGACTTCTTCTGGCGATGTTTTCCAGATGGAAAGGATgta---tgtattttaggtgttca-attcatatttatcaattatgt--tgattcttgacagtgggcatacttaatgattaatggcttgttgttag----------------
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0011g04160.t01 (Vitis vinifera), 5'ss of exon 5
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagttctaccattttatgttgct-tgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag
|| |||||||| ||||| ||| | || || |||| ||||||| ||| | ||| ||||||||||||||||||| || |||||||||||||| | ||| || || | | ||| | | | | | ||| |||| || || | || || || || | || ||| | | | || ||
TTCTGTGCTGATCACTGCGGTTATCACGGATGCAATAAAAGATGCAGTTGGACGGCCTCGGCCAGACTTCTTTTGGCGCTGCTTTCCTGATGGAAAAGATgtat-gtcaatatctatttcttaaccctagtt--tcttttcatgccttgttactgtgagaggtgaatatctttttcctcataatagtttgtgcagttgatctt-------
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0006g02480.t01 (Vitis vinifera), 5'ss of exon 3
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaa---atgtttatgcacaaatagttctaccattttatgttgcttgttatttgtcaattttgaaactgacaaggcactgttctggtaattt--tatctcag
||| || ||| |||| | ||| | ||| || |||| |||||||| || ||||| | ||||||||||||||||| |||||||||||||| ||| | ||| || || || | ||| | || | ||| | || | | || || | | |||||| | || || | | | || || || | | ||||
CTCTGTTCTGGTAACAGTGGTTATTACTGATGCAATAAAAAATGCAGTTGGTCGACCTCGACCAGACTTCTTTTGGCGTTGTTTTCCTGATGGGAAGGATgtatgcttctcacaaatgcaagttctttcatag-tagcttgttaatggaacagtattttttttgggacaatttc--acttggcatg---ttaattagggaacttaatgtgtcag
upper sequence: LOC_Os01g04660.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0011g04170.t01 (Vitis vinifera), 5'ss of exon 5
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagttctaccattttatgttgct-tgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag
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TTCTATGCTGATCACTGCGGTTATTACGGAAGCAATAAAAGATGCAGTTGGACGGCCTCGGCCAGACTTCTTTTGGCGCTGCTTTCCTGATGGAAAAGATgtat-gtcaatatctatttcttaaccctagtt--tcttttcatgccttgttactgtgagaggtgaatatttttttcctcataatagtttgtgcagttgatctt-------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|218497722|gb|FG949370.1|FG949370EST: GAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAG TTATATGATCAAGTGACAGGTGATGTGATTTGTCATGGAGAGAAAAGCTTC
genomic: GAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagtttt ... tttatctcagTTATATGATCAAGTGACAGGTGATGTGATTTGTCATGGAGAGAAAAGCTTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTCGGTGCTGATAACTGCAGTTGTAACTACTGTGGTAAAGAATGCAGTAGGAAGACCTAGGCCAGACTTCTTTTGGCGGTGTTTTCCTGATGGAAAGCAGgtagagttttcctcaaatgtttatgcacaaatagttctaccattttatgttgcttgttatttgtcaattttgaaactgacaaggcactgttctggtaattttatctcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA