Sequence
atgc intronic sequence ATGC exonic sequenceTTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g17350.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G053925_T01 (Zea mays), 5'ss of exon 3
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag
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TTGCTGGAGACGATGATAAAAAATTGTGGGGACGTTGTGCATATGGTTGTTGCTGAGAGAGACATACTTCATGAGATGGTCAAGATAGTAAAGAAAAGGgtatgtgcatacattttaaaccttaatttactgattgtc-----aatagcaaatcctt--------aatgcttc-tcttttgaaaattttag
upper sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 5'ss of exon 3
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaa-accttaaaag--ttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttg--agcttttag
| |||||||| || || || || ||||||||||||||||| ||||| ||||| |||| ||| | |||||||| |||||||||||||| ||||| | ||||| |||| || | || | || || ||| | | | || | | | |||| | | |||| | | || |||
CTGCTGGAGACAATCATAAAGAATTGTGGGGACATTGTCCACATGCATGTTGCCGAGAGAGATGTTCTTCATGAGATGGTGAAAATAGTAAAGAAGAAGgtattgatatttcttggatgttttcatagccttcctattttatacctgatt-tcatcatgaaaaatatgtttatcatatttatcacgcaaattgtag
upper sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 5'ss of exon 3
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag
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CTGCTGGAGACAATCATAAAGAATTGTGGGGACATTATCCACATGCATGTTGCCGAGAGAGATGTTCTTCATGAGATGGTGAAAATAGTAAAGAAGAAGgtattagttttcatggcattcctatt--ttatacctgatt---tcatcatgaaaagtatg---tttatcatatttatcacacaaa-ttgtag
upper sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 5'ss of exon 3
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaaccttaaaagttaaaattgtctggt-tagttgtaaactc--tttaaattttaacgccttattcttttgagcttttag---
|| ||||||| || || || |||||||| || ||||| || ||||| ||||| || | ||| | |||||||| |||||||||||||| ||||||| ||||| ||| || || || || | | |||| | | ||| || | |||| | | | | | | | || | |
TTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacataatttcttgaatattt----ttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtag
upper sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 5'ss of exon 3
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaac---cttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag
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TTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtatacatagtttcttgaatattttttcagttttctaatgtct--ctgttttcttcatatatatatgttgatgtcatttgtcataccaattgtag
upper sequence: LOC_Os02g17350.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 5'ss of exon 3
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatg-----tatataagtttaaaccttaaa------agttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag
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CTATTGGAGACAGTCGTAAAAAACTGTGGAGATATTGTCCATATGCATGTAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAGgtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagta----tttattctgc-aaaattgcagMapped 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|88419305|gb|CI599138.1|CI599138EST: TTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGG CCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatat ... gagcttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTACTGGAGACGATGATCAAAAACTGTGGGGACATTGTCCATATGCAAGTTGCTGAGAAAGACATACTTCATGAAATGGTGAAAATAGTCAAGAAAAGGgtatgtatataagtttaaaccttaaaagttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttgagcttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA