Sequence
atgc intronic sequence ATGC exonic sequenceTAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttttgcaagtgttctgttcttttagttgggcaagtgttctgtttcaactgctgtacactgaaaaatagcatattagtttcactttaatgg...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 8
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttt------tgcaa-gtgttctgttcttttagttgggcaa-gtgttctgtttcaactgctgtacactgaaaaatagcatattagtttc-----actttaatgg---------
|| | || ||||||||||| || || || || |||||||||||||||||||| || ||||| ||||| || ||||| ||||| ||||| |||||||| || | ||| | || | |||| || |||| | || || || | | | || || | ||| | | | || || | ||| ||
CAATAGGTCCAGTGAATTTCACCCAGAAGTGAGAAGAGTGAGGCGTGAAGGATCCTATATTTATGAGGAATTTATGCCAACTGGAGGGACAGATGTTAAGgtttggctgttttgagatttataatgctttctatttttttttctcttaaatgtatttggaatgtttgtccatatcctttagcatattagaatggtctcttagaattttcataaatgacttag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 6
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaaga----aaacttttgcaagtgttctgttcttttagttgggcaagtgttctgtttcaactgc-tgtacactgaaaaatagcatattagtttcactttaatgg---------------------------------------------------
||| | |||||||| || ||||| || || || ||||||||||||||||| || || |||||||||||||||||||| ||||| ||||| |||||||| || | || ||| | || |||| ||| ||| | || | || || | | || | | | || | | | | | || |
CAACAGGTCTAGTGAGTTCCATCCAGAGGTGAGAAGAGTGAGGCGTGAAGGGTCCTATATTTACGAGGAGTTCATGCCAACTGGAGGGACAGATGTTAAGgtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttt--tttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA18G49000.1 (Glycine max), 5'ss of exon 8
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttttgcaagtgttctgttcttttagttgggcaagtgttctgtttcaactgctgtacactgaaaaatagcatattagtttcactttaatgg----------------------------------------------------------
||| | |||||||| || ||||| || || || ||||||||||||||||| || || |||||||||||||||||||| ||||| ||||| |||||||| || || | | | |||| || | || || | | | ||| | || | | | | || | | |||
CAACAGGTCTAGTGAGTTCCATCCAGAGGTGAGAAGAGTGAGGCGTGAAGGGTCATATATTTACGAGGAGTTCATGCCAACTGGAGGGACAGATGTTAAGgtttgacta-tgaagtttatgttgctttgtgtttattttattgtttctttatttttttaattatatatttgggcttttttttttcagacacatgtgatgtttctacatagtttttcacaatagaaattcttttcaaacattttgacatatgattgtag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 6
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttttgcaagtgt-------tctgttcttttagttgggcaagtgttctgtttcaactgctgtacactgaaaaatagcatattagtttc-----actttaatgg----------
|| | || ||||||||||| || || || || |||||||||||||||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| || | | ||| | | | ||| ||| ||| | | || || | | | || || | ||| | | | || || | ||| ||
CAATAGGTCCAGTGAATTTCACCCAGAAGTGAGAAGAGTGAGGCGTGAAGGATCCTATATTTATGAGGAATTTATGCCTACTGGAGGGACAGATGTTAAGgtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 5'ss of exon 9
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttttgcaagtgttctgttcttttagttgggcaagtgttc-tgtttcaactgctgtacactgaaaaatagcatattagtttcactttaatgg----
|| ||||| ||||| ||||||||||||||||| ||||| ||| | ||||| ||||| || || |||||||| ||||||||||| || || ||||| || || | ||||| ||| | | | || | | | || || || || | || | ||| | ||| |||
GAATCGATCAAGTGAGTTTCATCCTGATGTCAGAAGAGTAAGGAGAGAAGGTTCTTATATATATGAGGAGTTTATGCCTACTGGGGGAACTGATGTCAAGgttgtga--tttttgttgctgtctagataagcttattctgttttaatccatgaccaggctacttaacctttct---taaaacattgaatgtgtttttatgctctt
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 5'ss of exon 9
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttttgcaagtgttctgttcttttagttgggcaagtgttctgtttcaactgctgtacactgaaaaat----agcatattagtttcactttaatgg
|||||||| ||||||||||||||||| ||||| || || ||| | ||||| ||||| || ||||||||||| ||| | || || || || ||||| || || | ||| | | | | ||| | | | | | | || || || ||| | || |||||| | | || ||
GAACCGATCAAGTGAATTTCATCCTGACGTCAGAAGGGTAAGGAGAGAAGGCTCTTATATATACGAGGAGTTTATGGCCACCGGAGGAACTGATGTCAAGgttctgattgtttcccttctacaca--tttttcgataaaaccattaccat-tcccatcttttggacaacataggcgtttgagaatattattgtacagttgttg-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|29674285|gb|CB670560.1|CB670560EST: GACGGATGTTAAA GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCA
genomic: GACGGATGTTAAAgtaagaaaac ... ctattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TAACCGATCTAGTGAATTTCATCCTGATGTCAGGAGAGTGAGGCGTGAAGGATCTTACATTTACGAGGAGTTCATGCCTACTGGTGGGACGGATGTTAAAgtaagaaaacttttgcaagtgttctgttcttttagttgggcaagtgttctgtttcaactgctgtacactgaaaaatagcatattagtttcactttaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata