Sequence
atgc intronic sequence ATGC exonic sequenceTGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactctgaaacttggtgagcttaggatctggatatatttttgtcggtattgcacttcctttttgtggattatttcttttgcactgataaggatgtg...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g46570.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G101181_T02 (Zea mays), 5'ss of exon 7
TGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactct-gaaacttggtgagcttaggatctggatatatttt-tgtcggtattgcacttcctttttgtggattatttcttttgcactgataaggatgtg
||| ||||||||||||||||||||||| |||||||| ||||| ||||| |||||| | | ||| || ||||||||||||||| ||||||||||| ||||||||||||||| ||||||||||||| || | ||| | | | | || | | | | ||| || | ||| | | | |
TGAACCTGACATGCTTGCATTTTCTGGCTGTTACTACGGTGGCGGTGAAAAAGAAAGAAAGGAATTGGGTGAAATTAGGAAACGATGGGATACATTACCTgtaagactcttgaaacttggtgagatttccctatggtttctccaaatactaatctgccatcagcatataattaatttttccattttttttctttttgctt--
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G15170.1 (Glycine max), 5'ss of exon 7
TGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactctgaaacttggtgagcttaggatctggatatatttt--tgtcggtattgcacttcctttttgtggattatttcttttgcactgataaggatgtg
||||| || ||||| |||||||| |||||||| | |||||||||||| |||||| | | ||| |||||||||| |||||||| ||| ||||| |||||||||| | || | | | || | ||| | || | || | | | ||| | || || | ||||| | ||
CGAGCCAGATATGCTGGCATTTTCAGGTTGTTATTTTGGTGGTGGTGAAAAAGAAAGACGCGAGCTAGGTGAAATCAGGAAAAGGTGGACAACACTGCCTgtaagaccacaatcctctgacttgtaataatgaaattctatcatactgacaagatgataatgattatttaaaactagttatttatttgctgattttgttg--
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G04720.1 (Glycine max), 5'ss of exon 7
TGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactctgaaacttggtgagcttaggatctggatatatttttgtcggtattgcacttcctttttgt--ggattatttcttttgcactgataaggatgtg----------------------
|||| | || ||||| |||||||| |||||||| | |||||||||||| |||||| | | ||| | |||||||| |||||||| ||| || | ||||||||||| | || | ||| | || | | | | || | | || || | || || |||| ||||| | || |
TGAGTCAGATATGCTGGCATTTTCAGGTTGTTATTTTGGTGGTGGTGAAAAAGAAAGACGCGAGCTTGGTGAAATCAGGAAAAGGTGGACAACGTTGCCTgtaagactgccatcctctg-acttctagtaataaaattttatcatattggcaagatgataataattagttaaaactagtttttttttgctgattttgttgagccattaccatgtggtaattcag
upper sequence: LOC_Os04g46570.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT4G16650.1 (Arabidopsis thaliana), 5'ss of exon 7
TGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactctgaaacttggtgagcttaggatctggatatatttttgtcggtattgcacttcctttttgtggattatttcttttgcactga-taaggatgtg----
||||||||||||||| || |||||||||||| ||| |||||| ||||| ||||| | ||| ||| ||||| || ||| ||||||| ||| | ||||| || | | | | | | ||| || |||| || | | | || | | | | | |||| | | | ||
TGAGCCTGACATGCTAGCCTTTTCTGGTTGTGACTTTGGTGGGGGTGAAAAAGAGAGAGCTGAGCTAGCAGAAATAAGAAAACGATGGGACACATTGCCTgtgagttcaatatgttcttttacataactttct-----taattttccaagttctctgcgttattcctctacggctctacctatgcaataaactgaaacttgatatMapped 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|25797606|gb|CA753567.1|CA753567EST: GGTGAAATTAGGAAAAGATGGGATACACTACCT GAGTTGAGCGCTGAGGATGAGCGCAGTAGGGGCAAATGTCCACTGACTCCT
genomic: GGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactct ... ttcctagcagGAGTTGAGCGCTGAGGATGAGCGCAGTAGGGGCAAATGTCCACTGACTCCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAGCCTGACATGCTTGCATTTTCTGGTTGTTACTATGGTGGTGGTGATAAAGAACGGAGGGAGTTAGGTGAAATTAGGAAAAGATGGGATACACTACCTgtaagactctgaaacttggtgagcttaggatctggatatatttttgtcggtattgcacttcctttttgtggattatttcttttgcactgataaggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG