Sequence
atgc intronic sequence ATGC exonic sequence...tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11840.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G141587_T03 (Zea mays), 3'ss of exon 21
-tcttattttcagacttacgc---gacactgtttaatt-tgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
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atgtgatattttgtctcaagtttagacttggcatcgctgtcttcaaattgcacgtctaagt-ttacgaaatgtgcactgatctgttc----catttgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCT
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G124886_T02 (Zea mays), 3'ss of exon 21
tcttattttcagacttacgcg-acact---gtttaatt-tgtaggagctatgtgttttattatctcac-catgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
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tggtatttgtggtctcaagtttagatttgagcataattgtcttcaaactgcaggtctaactttatgaaatgtgcattgttttgttc------catttgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTC
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
-tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctt--tatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| | ||| | | | | | ||||| | || | | |||| | | || | | | || | ||| || | |||| || || ||||| || ||||||||||| ||||||| || || ||||| ||||||||||| |||||| |||| || ||| ||| |||| | | |
agcatccgttctcattcatttgcc-ttgtttgggtagtcttatc-atgttgacaagtgacttatgg-attaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
---------------------------------------------------------------------------------------------tcttattttcagac--ttacgcgacactgttt--aatttgtagga-gctatgtgttttatt--atctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
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gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
tcttattttcagacttacgcgacact-gtttaatttgtaggagctatgt-gttttattatctcaccatgccttttttccttctcatgccattatctt--tatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
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----ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
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-----------gttcctttcaaatctttttaggttttagt-gtaatgtggtcaaggaga-caagttgtgggtttaagttaccttgcacttgaat--acagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
--tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
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catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatga--tttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAGMapped 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|29644063|gb|CB649070.1|CB649070EST: CGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAG GTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAAC
genomic: CGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctg ... atctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
atctcac putative branch site (score: 3)
ccttttttccttctca putative PPT
attatctttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - -tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccatt