Sequence
atgc intronic sequence ATGC exonic sequenceAGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgagggagattttttttatgtattaacactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g37430.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G350001_T01 (Zea mays), 5'ss of exon 11
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgaggga-------gattttttttatgtattaacactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata
||| |||||||||||| ||||||| |||||||||| |||||||||||||| || ||||| |||||||||||||| |||||||| || |||||||| |||||| | |||||| | ||| | ||| | | | | || || | || | | |||| || | ||| | | || | || | || ||
AGTTAATGGAACATCTGTTCTCTTCTTGCCTTGTGTTGTTTATAATTGGACCCCGCCTGAGGGTGCTGGACAGTTTCATGGTATACCCTTGGATGTTAAGgtataacatttt-cttacttgtaaggaacttaattggtcagtgttttgctctttttcttcatggaaataaatt--gtggcataatatt---aatagaaaatagtat-
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G038667_T02 (Zea mays), 5'ss of exon 8
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgagggagattttttttatgtatta-acactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata-----
||| |||||||||||| ||||||| ||||||||||| |||||||||||||| || ||||| |||||||||||||| |||||| | || |||||||| |||||| | |||||||| ||| | | | | | || | || || | || |||| | ||||| | || | || || || |
AGTTAATGGAACATCTGTTCTCTTCTTGCCTTGTGCTGTTTATAATTGGACCCCGCCTGAGGGTGCTGGACAGTTTCATGGTGTACCCTTGGATGTTAAGgtataacatttttcttacttgtaaagaacttaattggtcagtgttttgctcttttccttcatgga------aataaattatggcctagtgttaatagaaaatagta
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G143688_T01 (Zea mays), 5'ss of exon 5
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgaggga-------gattttttttatgtattaacactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata
||| |||||||||||| ||||||| ||||||||||| |||||||||||||| || ||||| |||||||||||||| |||||||| || |||||||| |||||| | |||||| | ||| | ||| | | | | || || | || | | |||| || | | | | | || | || ||
AGTTAATGGAACATCTGTTCTCTTCTTGCCTTGTGCTGTTTATAATTGGACCCCGCCTGAGGGTGCTGGACAGTTTCATGGTATACCCTTGGATGTTAAGgtataacatttt-cttacttgtaaggaacttaattggtcagtcttttgctctttttcttcatggaaataaatt-----gtggcctaatattaatagaaaatagtat-
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G42210.1 (Glycine max), 5'ss of exon 4
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacac--catttttcctacagatgagggagattttttttatgtattaacactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata--
| || || || | | || || |||||| | | || |||||||| |||||||| |||||||| || || ||||| ||||||||||||| |||||| | || || |||||| | | | | | | || | || | | || | || || | || | | || ||
TATTGGGGGTACCTCAGTAGTGTTCTTACCTTGTTCTTTGTACAATTGGACTCCACCTGAGGGTGCTGGTCAATTTCATGGCATGCCATTGGATGCTAAGgtatagtgcagacttattacaga---agtatttctgtctgatccttcgctggatgctttaagttagaattttggaaattttctgaatataa-tgttcctttagc
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G45320.1 (Arabidopsis thaliana), 5'ss of exon 5
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgagggagattttttttatgtattaacactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata
| | |||| | || | | ||| | || ||||| | || || |||||||| |||||||||||||| ||||| ||||| |||||||| ||||| ||||||| | | | |||| | | | | | | | || | || | | ||| || |||
AATAGCTGGAGCTTCAGTGTTATTTCTACCATGTGCTCTATACAACTGGACACCTCCTGAAGGTGCTGGTCAGTTTCATGGCATGCCATTAGATGTCAAGgtactctaaatc-ccta-aaaccataaa----ccctcaaagcatcatcagagtctcattactcgtttttttgcag-------------------------
upper sequence: LOC_Os06g37430.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0048g00310.t01 (Vitis vinifera), 5'ss of exon 6
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgaggg-agattttttttatgtattaacactaaaagaaaatggttttct--tagcaaattcttttgtacagctattaaaata-------------------------------------------------------------
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TATTGGTGGTACTTCAGTGCTCTTTCTACCTTGTGCTATTTACAATTGGACACCACCAGAGGGTGCTGGACAATTTCATGGCATGCCCCTTGATGTGAAGgtacataatttcttcaaatcattttttcacattgatcttggtcaatagctgagcttgaacatcatctttgggtatcccttgggtttgatccctttttaacatatatggcaagtttttatgagcatcattttttatttacgtctggctttgtttcctgtgcacagMapped 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|29671601|gb|CB667876.1|CB667876EST: CACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAG GTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAAT
genomic: CACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatt ... atgttgttagGTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGTGAATGGAACATCTATTCTCTTTTTGCCTTGTGCAGTTTATAATTGGACACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatttttcctacagatgagggagattttttttatgtattaacactaaaagaaaatggttttcttagcaaattcttttgtacagctattaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA