Sequence
atgc intronic sequence ATGC exonic sequenceTTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g11140.3 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaa-attattatagtagtactctttgtttcctgcat-gctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
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CTCCGTTGCCTCTTGTTCAAATCTGTGGGCTTTGATAATGGATGCTGGCACCGGATTTACTTCTCAAGTGTATGAACTGTCTCCATATTTTCTTCACAAGgtaagctattaaatgccccctttttggtattctagcaatctcacgtcacttttatttatttgttgtgctccctccttttcaaattatagctcactttggc---------------------------------------------------------------------------------
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgag-taattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagct---tacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
|||||||||||||| ||||| ||||| | || ||||||||||||||||| || || | ||||| ||||| || |||| || ||||||||||| | || || | || | || | | | | || | || || | |||| | | | || |||| | ||| | || || | | | |||| || || | | || | ||| ||||| | |||| |||
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACAGCACAAGTTTATGAACTCTCTCCCTTCTTCCTTCACAAGgttggctagtttatgttttagctgtggcattatgcgtgtgatgt-tggtgatatcatagtatcatgtttgtaactattatcattttatctgtatagtattttactaattttgttttgaacttaatgtagtctaacaaactcatgtttc----tttttaatag---------------------
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgag-taattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagct-tacact--ctcaataatagctaagtgtgattta-catggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
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CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTCTCTCCCCACTTCCTTCACAAGgttggctagtttatgttttagcggtggcattatgcgtgtggtgt-tggtgatatcctattatcatctttgtaactattatcgttttatctgtactgtattttactaatt-ttgtttttaacttaacgtaggctaacaaactcacgtttctgtttaatag-------------------------
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgag-taattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagct-tacact--ctcaataatagctaagtgtgattta-catggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
|||||||||||||| ||||| ||||| | || ||||||||||||||||| || || | ||||| ||||| || |||| || || ||||||||||| | || || | || | | || | | | | | | || || | |||| | | | | |||| | || | || ||| | | | |||| | | | | ||| | | | | ||| | ||| | || | |
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTGTCTCCCCACTTCCTTCACAAGgtttgctagtttatgttttagtggtggcattatgcatgtggtgt-tggtgatatcatattatcatctttggaactattatcgttttatctgtactgtattttactaatt-ttgtttttaacttaacgtaggctaacaaactcacgtttctgtttaatag-------------------------
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtttcc-tgcatgctcctatccttctcatcca-tcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgata-tgctcgcctatgatgctcttag
|| || |||||| |||| ||||||| |||| |||||||| |||||||| |||||| | ||||| ||||||||||| | ||||||||||||||||| || ||| | | || || | | | | | | | || | |||| || | |||| ||| | | || | | || | |||| ||| ||| | | | ||| || | || | | | | || |||
CAGTGTAGCGTCTTGTCAAAATTTGTGGGCGCTAATTATGGATGCAGGCACTGGTTTTACTGCACAAGTTTATGAGCTTTCACCCTATTTTCTTCACAAGgtgcgtctc----atttcttttgtttaacccatggcatacatatttatctttacatgtgtcatgcaattaaatttcatcagtatgatcgag-gcatattacaaggctacttctttcagcttac--tgttatacatttaattttaacaagtgatcaattaatctttttttgttctgtctatag
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
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TAGTGTGGCTTCTTGTTCAAACTTATGGGCCCTAATTATGGATGCTGGCACAGGCTTCAGTGCTCAAGTTTATGAACTCTCTCCTTATTTCCTTCACAAGgt---tgcttatattcctta-acaggca-----------ttgcatgttagcac--------ttcattgaacagtatgcatgtcacaaactggcacgtaaattgtgttgaaaacaagttaatactgtatttttgt-ctttgctgaag---------------------------------
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
|||||||||||| |||||||||||||| | || |||||||| || || ||||||||| ||||||| |||||||| || || || || ||||||||| || | | | ||| |||| | | |||| || | | || |||||| | ||| | | |||| | ||| |||| | |
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACAGGATTTACTGCTCAAGTTTATGAGCTGTCACATGTATTCCTCCACAAGgtgggtgtgtggtgtc-tcgctcaagt----tttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcac-----attgagtcatatttttacag------------------------------------------------------
upper sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtt--tcctgcatgctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
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CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag------------------------------------------------------------------------------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|218483459|gb|FG953851.1|FG953851EST: CTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAG GAATGGATAATGGATCAGTGGGAGAGAAACTTCTATATCACTTCATTAGCA
genomic: CTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaatt ... atgctcttagGAATGGATAATGGATCAGTGGGAGAGAAACTTCTATATCACTTCATTAGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtttcctgcatgctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT