Sequence
atgc intronic sequence ATGC exonic sequencegtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44200.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgta----acaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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---------------------------------------------------------------gtaattatactgattgcaaaacgcatagatacaac-tttgtgtcactatactcggcgcttctgataataatgtac-agGTTGAGTGGGATGAGATAAATGCTGCATGGGGTCAGGCTGCACTGCTGTTGCATACCATGGCTCAGTATTTCACCCCAAAATTCCA
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G027857_T01 (Zea mays), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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---------------------------------------------------------------gtaattatacagattgcaaaatacacagatacaac-tttgggtcactatagtgtttctgaaaatgatgtac-agGTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCG
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaaga---tgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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-------------------------------------ttatcctagagaattttcttaatcttgaattgaataatttttcttcctagtttgaatatttaagctttg-attatgatgttcacttt--tatgaaatgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCATACTATGTGCCAATATTTCCGACCGAAGTTTCA
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgt-taatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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-----------------------------tttatcctagagaattt--tcttaatcttgaactgaatcctttttcttcct--agtttgaatattgaagctttgattatgatgttactattatgaaa-----tgtttagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTCCTTCTTCACACTATGTGCCAGTATTTCCGACCGAAGTTTCA
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G61710.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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-------------------------------------gtaagttttgctactttccttgtat---gtttataatct---cgttctgctcatatt-----tttgtct-----aaacaac-atgaaacatattt---agGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCA
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA--------------
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-------------------------------------gtaagttttgctactttccttgtat---gtttataatct---cgttctgctcatatt-----tttgtct-----aaacaac-atgaaacatattt---agGTTGAGTGGGATGAGATCAATGCTGCTTGGGGCCAAGCCTGTCTTCTCCTCCATACGATGTGTAACTATTTCCGGCCAAAGTTTCAGTATCCTTATAACT
upper sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 6
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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--------------tatgtcatcaactagtatacagcttattttagaatactttccttga----tattggaactg---aggcaccgactaagaagtttatctgtactgtggaaaca----------------tatagGTTGAATGGGATGAGATAAATGCTGCCTGGGGCCAAGCTTGCCTTCTTCTCCATACAATGGTTCAATATTTCCGACCAAAGTTCCAMapped 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|33807311|gb|CF329536.1|CF329536EST: TGATCGGAACAATAAACAACTTTCGTCTTGGCCGCCTTCCTAATGTACAG GTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTG
genomic: TGATCGGAACAATAAACAACTTTCGTCTTGGCCGCCTTCCTAATGTACAGgtaattatgc ... cttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
atgtaac putative branch site (score: 3)
tgttactcttttctt putative PPT
ttaatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatgcaaaatgtgcagatatcacgtccattcactatcttttagtgctttccttgaattctattcaagatgtacatggaatgttcatgttgatcctttgtgttaatgtaacaactgtgttactcttttcttagGTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGA
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