Sequence
atgc intronic sequence ATGC exonic sequence...cctgttttttttttttcagaatcatcactagcttcgctctgttcttaatatttatttatgggccatttggcatctgagcaaaaattttcctattgtgcagGTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTGCTGCGGACTTGCTGAGAGCAAACAAATCTTCAATTTGCTTATATGTTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g45730.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
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|88227997|gb|CI227477.1|CI227477EST: GTTGACTGACCTTGTCAAGGTTGCCCGTGGAAGAAAGAATTAAAATGCAG GTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTG
genomic: GTTGACTGACCTTGTCAAGGTTGCCCGTGGAAGAAAGAATTAAAATGCAGgtacgtgcgt ... tattgtgcagGTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTG
EST:
gi|86493245|gb|CI135878.1|CI135878EST: GTTGACTGACCTTGTCAAGGTTGCCCGTGGAAGAAAGAATTAAAATGCAG GTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTG
genomic: GTTGACTGACCTTGTCAAGGTTGCCCGTGGAAGAAAGAATTAAAATGCAGgtacgtgcgt ... tattgtgcagGTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatttatttatgggccatttggcatctgagcaaaaattttcctattgtgcagGTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTGCTGCGGACTTGCTGAGAGCAAACAAATCTTCAATTTGCTTATATGTTTG
tcttaat putative branch site (score: 3)
ttttcctatt putative PPT
aaaaattttcctatt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgttttttttttttcagaatcatcactagcttcgctctgttcttaatatttatttatgggccatttggcatctgagcaaaaattttcctattgtgcagGTAATAAGCAGAGAAGATTTCAAGTTGCTCCTGGATGCTGGCGATGAGCTGCTGCGGACTTGCTGAGAGCAAACAAATCTTCAATTTGCTTATATGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - -cactagc
- - - - - - - - - - - - - - - - - - - -tgttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagcaaa