Sequence
atgc intronic sequence ATGC exonic sequenceCCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtgctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60040.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G068755_T02 (Zea mays), 5'ss of exon 8
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtg--ctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag
||||| |||||||||||||||| || |||||||||||||| || || ||||| ||||| || ||||||||||| ||||| ||||||||||| | ||| |||| |||| || | | ||||| || || ||||| | || | | | | | ||||||| |||||| |||
CCCCTGTGGAGATCGATGAATATGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTCTGGGACGGTGTGgtatgggacctgtcttgaatgca-------cacgctattggtcacactatcgta-tgaaaagtagttattatattagt-------ttttgttgtctgatgtcag
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G070126_T02 (Zea mays), 5'ss of exon 8
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtg--ctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag
||||| ||||||||||||||||||| |||||||||||||| || || ||||| ||||| || ||||||||||||||||| ||||||||||||| ||| |||| |||| || | | |||| || ||| ||||| | ||| || | ||| ||||| | | |||| ||||
CCCCTGTGGAGATCGATGAATACGACCTTGTTGATCCTGTAGACATTTTAACCCCACTAGAAAAGTCTGGATTTTGGGACGGTGTGgtatgtgacctgtcttgaatgca---------cactattggccacactatcata-tgaaaagtagtcatcat-------attggtttttggtgtgtgatgccag
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 8
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgt--atgtgctgatttgagtgcagcattg-atacattgtccatcaca---acattatagtgaaata----ttgtcctcttttgaatgattctat-tttgttatctgat-accag----
| ||| || ||||| ||||| || |||||||||||||||||||| || || || | ||||||||||||||||||||||| ||||| | | ||| | | |||| | || | | || | ||| |||| | || | || | | | |||| | || || ||| || | |
CTCCTCAAGAAATCGACGAATATGAACTTGTTGATCCTGTTGATATATTGACTCCTTTGGAGAAGTCTGGATTTTGGGATGGAGTGgtcagttttctgtcccatctctcggattgtactcagtaattaatgcacctatattttagttatatgggtttgaatctatctcagtttgttctttactttttgtcttattaatattcag
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G29520.1 (Glycine max), 5'ss of exon 5
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgt--atgtgctgatttgagtgcagcattg-atacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag
| ||| || ||||||||||| || |||||||||||||||||||| || || || | |||||||| |||||||||||||| || || | | ||| | | |||| | || | | | || | |||| | | | ||||||| ||| | || |||
CTCCTCAAGAAATCGATGAATATGAACTTGTTGATCCTGTTGATATATTGACTCCTTTAGAGAAGTCAGGATTTTGGGATGGAGTTgttagttttctgccccatctcttggattgtactcagtaactaatgcacctttattttag----ctatatgagtttgaatatgtct-tgttaatattcag------
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 8
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgt--atgtgctgatttgagtgcagcattg-atacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag
| ||| || ||||| ||||| || |||||||||||||||||||| || | || | |||||||| |||||||||||||| || || | | ||| | | |||| | || | | | || | |||| | | | ||||||| ||| | || |||
CTCCTCAAGAAATCGACGAATATGAACTTGTTGATCCTGTTGATATATTGATTCCTTTGGAGAAGTCAGGATTTTGGGATGGAGTTgttagttttctgccccatttctcggattgtactcagtaactaatgcacctttattttag----ctatatgagtttgaatctgtct-tgttaatattcag------
upper sequence: LOC_Os01g60040.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv10s0116g00490.t01 (Vitis vinifera), 5'ss of exon 8
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtgctgatttgagtgc--agcattgatacattgtccatcacaac-------attatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag---------------------------
| ||| ||| || |||||||| || ||||| |||||||||||||| || || || | || ||||| |||||||||||||| ||||| ||||| | | | | | || || || | | | || || | | |||| ||| | ||| || || || |||||| || ||
CTCCTCAGGAAATAGATGAATATGAACTTGTCGATCCTGTTGATATATTGACCCCTTTAGAAAAGTCAGGATTTTGGGATGGAGTGgtcagtgctttctctctctctcatctcttattcagtgacatttgctacttattttgttgtgttttaatactgttgttattttgatctctcaatcatgttattagaggttagttctttaacattttgtttgtcctttagMapped 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|86490173|gb|CI132806.1|CI132806EST: CTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTG AAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAA
genomic: CTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtgctg ... ctgataccagAAAGCTACCAAGTGGTCTGAAAGAAGGGATGCTGTTGCCGAGCTAACCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCCCTATGGAGATCGATGAATACGATCTTGTTGATCCTGTTGATATCTTAACACCACTTGAGAAGTCTGGATTTTGGGATGGTGTGgtatgtgctgatttgagtgcagcattgatacattgtccatcacaacattatagtgaaatattgtcctcttttgaatgattctattttgttatctgataccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT