Sequence
atgc intronic sequence ATGC exonic sequenceGTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaatttagctaacatttatgtagacttctaatttatcactaacatagtttgttttggttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54100.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G120951_T01 (Zea mays), 5'ss of exon 5
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaatttagctaacattt-atgtagacttctaatttatcactaacatagtttgttttggttttcag
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GTTATGGATATGCTCGGACCCAGTCTGTGGGATGTCTGGAATAATAAATCTCACATgtgagtcatagttttgagtgaacacgtgatattgacttttagtttaccgttaacatcatt--cttttgttagcag
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G01890.1 (Glycine max), 5'ss of exon 5
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaatttagctaacatttatgtagacttctaatttatcactaacatagtttgttttggttttcag--------------------------------
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GTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCAgtaagtccttgaaattatgtcagatatgaataaaattgtattcttt-------gtagttgattttgactttcagttgctgtgctaatgtgtttttctgaattccag
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G21570.1 (Glycine max), 5'ss of exon 5
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaatttagctaacatttatgtagacttctaatttatcactaacatagtttgttttggttttcag--------------------------------
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GTTATGGATATGCTGGGACCTAGCCTCTGGGACGTTTGGAATAATAGCAATCATCAgtaagtccttgaaattatgtcagatatgaatacaattgtatacttt-------gtagttgattttgactttcagttgctgtgctaatctgtttttctgaattccag
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 5
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttt-----tccaattta-gctaacatttatgtagacttctaatttatcactaacata----gtttgttttggttttcag-------------------------
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GTTATGGATATGCTTGGACCTAGTTTGTGGGATGTTTGGAATAACAACTCACACACgtaagtttctttttcaaatatgtggcggaaagtgtgttatcttttagtttatatgtaacacatgcaatttactcttatctaatgtttactttcactttgtcaatttcag
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 5'ss of exon 5
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagtt---ttccaatttagctaaca--tttatgtagacttctaat----ttatcactaacat-agtttgttttggttttcag---------------------------
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GTTATGGACATGCTTGGACCAAGCTTGTGGGATGTTTGGAATAATAACTCTCACACgtgagtgagatgaaaatatgatttattattttttatatgctacaaatggttctgttgcttttaccattttgtgcttgtatttgcctaatgaagatatttgcttaattccag
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaat-ttagctaacatttatgtagact--tctaatttatcactaacat--agtttgttttggttttcag--------------------------
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GTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGCgtaagtgacgctctattgacaggcttttcgcttgaataatgtggccttcgatcgacattcaattactttttactgtgaaactgaagttcgattatctttctgcag
upper sequence: LOC_Os01g54100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S39_28V6.1 (Physcomitrella patens), 5'ss of exon 2
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaatttagctaacatttatgtagacttctaatttatcactaacatagtttgttttggttttcag
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ATCAGGGATATGCTTGGACCAAGTCTCTGGGATGTTTGGAACTCTTCAGATCAAGCgcaagtattt-aaggcaactcgttctaat---------caaacaagtatgtacatag-----------------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|58680661|gb|CK069348.1|CK069348EST: GATATGCTGGGA-CCAGTCTTTGGGATGTTTGGAATAATAATTCTCATAC AATGTCTGTTGAGATGGTGGCGTGCATCGCTATTGAAGCTATCTCCATACT
genomic: GATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttc ... tggttttcagAATGTCTGTTGAGATGGTTGCGTGCATCGCTATTGAAGCTATCTCCATACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTATGGATATGCTGGGACCCAGTCTTTGGGATGTTTGGAATAATAATTCTCACACgtgagttttccaatttagctaacatttatgtagacttctaatttatcactaacatagtttgttttggttttcag
- - - - ATGCTG