Sequence
atgc intronic sequence ATGC exonic sequenceGATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtacatattcttgatttagaaaagacactttttccctccatttagcccatgttctgtgctgatatgaacttgagttgccttcaatatttacacattatttgttaaccag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g01630.6 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA16G00590.1 (Glycine max), 5'ss of exon 8
GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtac--atattcttgatttagaaaagacactttttccctccatttagcccatgttctgtgctgatatgaacttgagttgcc----ttcaatatttacacattatttgttaaccag--------------------------------------------------------
|||||||| || || || |||||||| ||||||||||| | || || || || |||| ||| ||||| || |||||||||||||||||||||||| |||| | | | | || || | | ||||| || | || | | |||| | ||||||| | ||| | | | |
GATAAAGCCACTGTTGAAATGGAATGTATGGAGGAAGGTTTTCTGGCCAAGATAATCCGTGGGGATGGGGCAAAAGAAATTAAAGTTGGTGAGgtattgatatcttctagctctcccctcctctcttctttggaaaggactttttgttcgttgttc-catagtttgaaattgcaagaataaaatattttggctttacacgctgaactttattgacatatgaaaggcatcatcagtattggtaacatgaagaatttctttcatag
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA07G03930.1 (Glycine max), 5'ss of exon 8
GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtac--atattcttga--------------tttagaaaagacactttttccctccatttagcccatgttctgtgctgatatgaacttgagttgccttcaatatttacacattatttgttaaccag--------------------------------------------
|||||||| || || || |||||||| ||||||||||| || || || || || |||| || ||||| || |||||||||||||||||||||||| |||| | | | | |||| ||| || | | | | | ||| | | | | || | ||| ||| | | | || ||||| | |
GATAAAGCCACTGTTGAAATGGAATGTATGGAGGAAGGTTATCTGGCCAAGATAATCCGCGGGGATGGGGCAAAAGAAATTAAAGTTGGTGAGgtattgatatcttctagctctcctctcttctctggaaaggacttgttattcgttgttccatagtatga--aattgtaagaaaaaaatattttggctttacactctgaactttattgacatatgaaaggcataatcacagtattggttacatgaataatttctttcatag
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 5'ss of exon 8
GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtacatattcttgatttagaaaagacactttttccctccatttagcccatgttctgtgctgatatgaacttgagttgccttcaatatttacacattatttgttaaccag
|||||||| || || ||||||||||||||||||||||| || |||||||| || | | ||||||||| || ||||| || |||||||| ||||| | |||| || || | |||| || ||| | | | | || ||| | | | | | |||| || || || | |
GATAAAGCAACTGTTGAGATGGAATGCATGGAGGAAGGATATCTTGCTAAGATAGTACTTGGAGATGGGGCAAAAGAGATCAAAGTTGGGCAGgta-gtcttctgaatgctgacatattg--ttttagtagcacgtagttc-taaaatatattggtatagatctctttaactt---gtattgtcatatgatgggccagtg--
upper sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 9
GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtacatattcttgatttagaaaagacactttttccctccatttagcccatgttctgtgctgatatgaacttgagttgccttcaatatttacacattatttgttaaccag
|||||||| ||||| ||||||||||||||||| ||||| ||||||||||| || || || |||||||| || |||||||||||||||||||||||| | | || |||| | | || | | || | | | | | | | || || ||| ||| || | | || | ||
GATAAAGCAACAGTTGAGATGGAATGCATGGAAGAAGGATACCTTGCTAAGATAATTCAAGGAGATGGGGCAAAAGAAATTAAAGTTGGTGAGgtat-tgctttt-atttgtcactaaggtcacttggttgctattgtctaactctttctttcaa----agct--agctgctttctat-ctcatgtgtttgccagccatcaaMapped 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|58669994|gb|CK058680.1|CK058680EST: TTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAG ATTATTGCCGTAACCGTGGAAGAAGAGGAAGACATCGGCAAATTTAAGGAT
genomic: TTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtacatattc ... tgttaaccagATTATTGCCGTAACCGTGGAAGAAGAGGAAGACATCGGCAAATTTAAGGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATAAAGCGACAGTGGAGATGGAATGCATGGAGGAAGGCTACCTTGCTAAAATTATCCATGGAGATGGTGCCAAAGAAATTAAAGTTGGTGAGgtacatattcttgatttagaaaagacactttttccctccatttagcccatgttctgtgctgatatgaacttgagttgccttcaatatttacacattatttgttaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA