Sequence
atgc intronic sequence ATGC exonic sequencegtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g18310.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttt-tccatgtgtcct-ctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
||| ||| | | | | ||| || || | | |||| |||| ||| | ||| | ||| | ||||| ||| ||| || |||||||||||||||||| |||||||| || || ||||| |||||||||||||||| || |||||||||||||||| ||||||||||||||||||
----gttagctatcataggtgataaaataggcctagcaagactgc-tctctacttatagaagtgttaccaaa-actaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 19
gtcagttt---gctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttag-ctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
|| ||| | | || || || | | | || | || ||| ||| | |||| | |||| || | || | | |||||||||||||||||||||||||| ||||| || || | |||||||| ||||| || | ||||| ||||||| | || || || |||||
gttagtgtcataattaagtttatggttgtgtacattcatgctatttatttcacaagaaataggttgacaaatgt-acacattttgacttactatctatatgttagATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGA
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 24
gtcagttt---gctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttag-ctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
|| ||| | || || || || | | | || | || | | ||| | |||| | |||| || | || | | |||||||||||||||||||||||||| |||||||| || | |||||||
gttagtgtcatacttaagtttatggttgtgtacagtcatgctatttatttcacgagaaataggttgacaaatgt-acacattttgacttactatctataagttagATACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATG----------------------------------------------
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 29
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
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---------------gttagtgccatccttaagtcaggaaatatggattga--caaaagtatacattattagtgctcctgcacttactatctatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGA
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 20
gtcagtttgctctaggaaatta---ccaaactcaagtaagaaaattttgtctcaacttttag-ctatcaaacctg-acactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA-
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-ttagtgtcatacttgaatttaaagttgtgtgcagtcatgttatttatttcacaagaaataggttgacaaatttacacgttgacttactatctatatatgtc--agaTACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAG
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
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----------gttagtgtcatccttaattcagg-aaatatggattgactaaagtatacgttattagtgct----cctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 18
-gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
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tagcttttgaatttagaaaaatttggtggataaccaacaaatctaggaatttg--tgtggaaatgagtatagaaaattctataacttttttacttttggtagATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAMapped 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|25044722|gb|AJ420705.1|AJ420705EST: TTGGATTTCCTAAG ATACAATGGGCGTGCACTTTGATGAAATAAACGTCTGGCATCTGTGATGGG
genomic: TTGGATTTCCAAAGgtcagtttgc ... tgtcctctagATACAAT-GGCGTGCAC-TTGATGAAATAAACG-CTGGCATCTGTGATGGG
EST:
gi|58672416|gb|CK061102.1|CK061102EST: CACTCCAGAGGTCAATATTAACAGCGCAGCCTATCATTGGATTTCCAAAG ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATG
genomic: CACTCCAGAGGTCAATATTAACAGCGCAGCCTATCATTGGATTTCCAAAGgtcagtttgc ... tgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATG
EST:
gi|88431147|gb|CI574318.1|CI574318EST: CACTCCAGAGGTCAATATTAACAGCGCAGCCTATCATTGGATTTCCAAAG ATACAATGGGGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATG
genomic: CACTCCAGAGGTCAATATTAACAGCGCAGCCTATCATTGGATTTCCAAAGgtcagtttgc ... tgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
acctgac putative branch site (score: 3)
tgtcctct putative PPT
actttta TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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