Sequence
atgc intronic sequence ATGC exonic sequenceTTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g45840.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 3
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag---------
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TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattcaagtacct-agctatttgggacttttt----------ttttctagtttacgagtgatgactagacctatttagctcctgcag
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G170148_T01 (Zea mays), 5'ss of exon 3
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag
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TTCTTGAAGGTTCAGAAGAATGGCACAGGCGAGCATCTGCCCCCACCCAGGCCAAAACGGAAGGCAGCTCATCCATATCCCCAGAAATCATCTAAAAATGgtctgcgttattcaaggacct-agctacttggcatgttttttttctagataacaagggatgactaa-attcatttggcttctgcag
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G057408_T02 (Zea mays), 5'ss of exon 3
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag
|| ||||||||||||| |||||||| || || |||||||| |||||||||||||| || ||||||||||||||||||||||||||||| ||||||||||||||||| | ||| ||| || | | | ||||| ||||||||| ||| | | || |||||||
TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattcaagtacct-agctatttgggacttttt----------ttttctagtttacgagtgatgactagacctatttag
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G37520.1 (Glycine max), 5'ss of exon 3
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag
||| | || |||||||| | ||| ||| |||||||||| ||||||||||| ||||| | || || | |||||||||||| ||||| || || |||||||||| | | | ||| | | | | | |||| ||| | ||| | | | ||| || | || |
TTTCTAAAAGTTCAGAAGAGTGGGACAAGTGAACATCTTCCTCCACCCAGACCAAAAAGAAAAGCTGTTCATCCATATCCTCAGAAAGCTTCAAAAAATGgttagaa-tcttcactatattttttgctacacaatttagtgcatttg--tatctaataattgttagtgatatttggcag-------
upper sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G30250.1 (Glycine max), 5'ss of exon 3
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag---
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TTTCTAAAAGTTCAGAAGAGTGGGACAAATGAACATCTTCCTCCACCCAGACCAAAAAGAAAAGCTGCTCATCCATATCCTCAGAAAGCTTCAAAAACTGgtt-atagtcttcacta----tattttttttttttgctacacaatttagtgcatttgtctct--aataattgttggtgagatttggcagMapped 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|33678202|gb|CF306441.1|CF306441EST: GCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATG CTTGTGCAGTTTCGCCAGCTGCTATATCACAACCCCCTCCTCTGGGGGAGC
genomic: GCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactg ... aattatttagCTTGTGCAGTTTCGCCAGCTGCTATATCACAACCCCCTCCTCTGGGGGAGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA