Sequence
atgc intronic sequence ATGC exonic sequenceCAAGGGAGAATTAGATGAGCGCATGTTCGCAAACGATGAGGACAGCTTGCTTGGCAGTGGAAGTCTGTCAGGAGGTGCCATCAATTTACCAGGCACAAAGgtaattagtgttaagcctacacatgttcattcaacttaaaaccccaaatcttatgttttaactttacctgtgggtattgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42600.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42600.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G016997_T01 (Zea mays), 5'ss of exon 9
CAAGGGAGAATTAGATGAGCGCATGTTCGCAAACGATGAGGACAGCTTGCTTGGCAGTGGAAGTCTGTCAGGAGGTGCCATCAATTTACCAGGCACAAAGgtaatt---agtgttaagcctacacat--gttcattca--acttaaaaccccaaatcttatgttttaactttacctgtg----ggtattgcag
| || || |||||||||||||||| || || ||||||||||| || |||||||||||||| || ||||| || ||||| ||||||||||||||||||||||| | | | | || ||| || |||| |||| ||| | | || | || || || | || |||||| |||
AAGAGGCGAGCTAGATGAGCGCATGTTTGCTAATGATGAGGACAGTTTACTTGGCAGTGGAAGCCTTTCAGGTGGAGCCATTAATTTACCAGGCACAAAGgtaatactgattagtgaaattattcattcattgcttcataacttgaaagattagaaattct-ttaaaatcgtatgtatgtcgtggtatttcag
upper sequence: LOC_Os08g42600.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G033828_T02 (Zea mays), 5'ss of exon 10
CAAGGGAGAATTAGATGAGCGCATGTTCGCAAACGATGAGGACAGCTTGCTTGGCAGTGGAAGTCTGTCAGGAGGTGCCATCAATTTACCAGGCACAAAGgtaatt---agtgttaagcctacacat--gttcattca--acttaaaaccccaaatcttatgttttaactttacctgtg----ggtattgcag
|| || || |||||||||||||||| || || ||||||||||| || ||||| |||||||| || ||||| || ||||| ||||||||||||||||||||||| | |||| || ||| | |||| |||| || | | | || || || | || | || |||||| |||
AAAAGGTGAGCTAGATGAGCGCATGTTTGCTAATGATGAGGACAGTTTACTTGGTAGTGGAAGCCTTTCAGGTGGAGCCATTAATTTACCAGGCACAAAGgtaatactaaccaggaagcttattcatccactgtttcataacttggaagctttgaaatcat-ttaaaattgtatgtatgctgtggtatttcagMapped 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|29622543|gb|CB627554.1|CB627554EST: TTGGCAGTGGAAGTCTGTCAGGAGGTGCCATCAATTTACCAGGCACAAAG AGAAAGTACGATGTTATGGCCTCACCTGCAAAATCAATAACAAGTCCAAGT
genomic: TTGGCAGTGGAAGTCTGTCAGGAGGTGCCATCAATTTACCAGGCACAAAGgtaattagtg ... ggtattgcagAGAAAGTACGATGTTATGGCCTCACCTGCAAAATCAATAACAAGTCCAAGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAAGGGAGAATTAGATGAGCGCATGTTCGCAAACGATGAGGACAGCTTGCTTGGCAGTGGAAGTCTGTCAGGAGGTGCCATCAATTTACCAGGCACAAAGgtaattagtgttaagcctacacatgttcattcaacttaaaaccccaaatcttatgttttaactttacctgtgggtattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG