Sequence
atgc intronic sequence ATGC exonic sequenceTTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcgcttcattagtttgctcttatctgtttgcataagacggatcgttttgttctatattttcatacctagtactatcaaagcttcctctgaact...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08400.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G017845_T04 (Zea mays), 5'ss of exon 6
TTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcgcttcattagtttgctcttatctgtttgcataagacggatcgttttgttctatatttt-cataccta---gtactatcaaagctt-cctctgaact-----------------------------------------------------------------------------
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TTCTCCATGTCCGGGAATCATCCATACCATAAAACTTGCTACAAGGAGCAGTTTCACCCGAAATGTGATGTCTGCAAGCAGTTCgtaaggatcactttatttaccctgaccgatctgtttatgctata-agttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcag
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G36620.1 (Glycine max), 5'ss of exon 5
TTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcgcttcattagtttgctcttatctgtttgcataagacggatcgttttgttctatattttcatacctagtact-atcaaagcttcctctgaact
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-TCTCCACATCTGGGAATTACCCTTACCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTCGtaagtattaactagttttcgggaaaattgcacttggtaccccttagattttcttatatgacatgcacacccatgctatttattacttgttacttgttacc
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA14G08450.1 (Glycine max), 5'ss of exon 6
TTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcgcttcattagttt----gctcttatctgtttgcataagacggatcgttttgttctatattttcatacctagtactatcaaagcttcctctgaact
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TTTTCCACATCTGGGAATTACCCTTATCATAAATCATGCTATAAGGAAAGCTACCATCCAAAATGTGATGTCTGCAAGCACTTCgtaagtatt-tttaacaagttttagggaaaattgcacttggtaccccttagatttgcttatatgacatgcacacccatgctattttttgacctgtcacttg---
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 5'ss of exon 6
TTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtc------gcttcattag------tttgctcttatctgtttgcataagacggatcgttttgttctatattttcatacctagtactatcaaagcttcctctgaact
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TATTCTATGAATGGGAATTACCCTTATCACAAATCTTGCTACAAGGAGCACTATCACCCAAAATGTGATGTTTGCAAGCACTTTgtaagtatctgtccggcttgaggaaaaaaattttcttgccatatattttaatacaaagcatgatgctctcttagagtctt---ccttttcctgtcaaatgctg---------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|56158549|gb|AU095148.2|AU095148EST: CATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTT ATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGG
genomic: CATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcg ... tcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCTCCATGTCGGGAAACCATCCATACCATAAAACATGCTACAAGGAGCGCTTTCACCCAAAATGTGATGTCTGCAAGCAATTTgtaagagtcgcttcattagtttgctcttatctgtttgcataagacggatcgttttgttctatattttcatacctagtactatcaaagcttcctctgaact
- - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA