Sequence
atgc intronic sequence ATGC exonic sequenceTTGCTGCGTCAAGGTGGCCGTCCATGTCCGCCCGCTCATCGGCGACGAGAAGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAGgtattccttctcttctctttttatcactcactcatttggcttcttttttcttgtttatacgtcccaattcagagagactagattgactctcatcctgtca...
Basic information
species | Oryza sativa |
transcript | LOC_Os09g02650.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G026218_T02 (Zea mays), 5'ss of exon 1
TTGCTGCGTCAAGGTGGCCGTCCATGTCCGCCCGCTCATCGGCGACGAGAAGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAGgtattccttctcttctctttttatcactcactcatttggcttcttttttcttgtttatacgtcccaat-tcagagagactagattgactctcatcctgtca----
|||||||||||||||||| ||||| | ||||| |||||||||||||||||||| ||||||||||||||||||||| ||||||| | |||||||||||||||| |||| | ||| || || | || | | | | | | | || | || || || | | |||||
TTGCTGCGTCAAGGTGGCGGTCCACGCGCGCCCCCTCATCGGCGACGAGAAGCTGCAGGGCTGTAAGGACTGCGTCGCCGTCGTGCCGGGCAAGCCGCAGgtatcgattctgcgacttcttt---gcttcttcgctgggga--gtgggccgggcatgaatcttcggatgtttctgaacctgtgtttcccgccctcctgcgtgtgc
upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA04G04380.1 (Glycine max), 5'ss of exon 1
TTGCTGCGTCAAGGTGGCCGTCCATGTCCGCCCGCTCATCGGCGACGAGAAGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAGgtattccttctcttctctttttatcactcactcatttggc-ttcttttttcttgtttatacgtcccaattcagagagactag-attgactct-catcctgtca
||||||||||||||| || || ||||| || || ||||||| ||||||||||||||| || || || ||||||||| ||||||| || || ||||||||||| | | |||| | ||| || ||| | ||| | | | | | | | || | | | | |||||| || | |||
TTGCTGCGTCAAGGTCGCGGTTCATGTACGGCCACTCATCGCCGACGAGAAGCTTCAAGGATGCAAAGACTGCGTCACCGTCGTTTCAGGGAAGCCGCAGgtgcacttactctctcaactcaatcgtg---tcgtttaaccttcgctatagtcaaatgtgaatacgaactgaagtgcattgtcgttgacttgacagtgtttca
upper sequence: LOC_Os09g02650.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA06G04520.1 (Glycine max), 5'ss of exon 1
TTGCTGCGTCAAGGTGGCCGTCCATGTCCGCCCGCTCATCGGCGACGAGAAGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAGgtattccttctcttctctttttatcactcactcatttggc-ttcttttttcttgtttatacgtcccaattcagagagactag-attgactctcatcctgtca
||||||||||||||| || || ||||| || || ||||||| ||||||||||||||| || || || ||||||||| || |||| || || ||||||||||| | || ||||| || || ||| | ||| | | | | | | | || | | | | |||||||||
TTGCTGCGTCAAGGTCGCAGTTCATGTACGGCCACTCATCGCCGACGAGAAGCTTCAAGGATGCAAAGACTGCGTCACCATCGTTTCAGGGAAGCCGCAGgtgcatacttact-ctcttaactcaacggtatcgtttaaccttcgctatagtcaaatgtgaatacgaactgaagcgcattgtcgttgactctcccgacagt-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|29639363|gb|CB644372.1|CB644372EST: AGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAG GTTCAGATCGGGAGCCATTCCTTCACCTTCGACCATGTGTACGGCAGCTCC
genomic: AGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAGgtattccttc ... gttgttgcagGTTCAGATCGGGAGCCATTCCTTCACCTTCGACCATGTGTACGGCAGCTCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGCTGCGTCAAGGTGGCCGTCCATGTCCGCCCGCTCATCGGCGACGAGAAGCTTCAGGGCTGTAAGGACTGCGTCTCCGTCGTCTCCGGCAAGCCGCAGgtattccttctcttctctttttatcactcactcatttggcttcttttttcttgtttatacgtcccaattcagagagactagattgactctcatcctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctct