Sequence
atgc intronic sequence ATGC exonic sequenceTCCAACAAGACCTAATCCTGCAGCAGGGGGAGAATTATGCGCAGAGACAGGAATAGGTGTATTTTTGAGCAAGgtgagtgtctgaccatactttttgttcaaaaataagtgtctgaccataatttatgttcaaaaataagtgtctgaccttaaagtgccttaatatgcactaaaattcttactgatcgcactgcaatgtttttgtcctgcgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g42600.1 |
intron # | 12 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g42600.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G033828_T02 (Zea mays), 5'ss of exon 13
TCCAACAAGACCTAATCCTGCAGCAGGGGGAGAATTATGCGCAGAGACAGGAATAGGTGTATTTTTGAGCAAGgtgagtgt--ctgaccatacttttt---gttcaaaaataagtgtctgaccataatttatgttcaaaaataagtgtctgaccttaaagtgccttaatatgcactaaaattcttactgatcgcactgcaatgtttttgtcctgcgcag
||||||||| || ||||||||||| || || ||| || ||||||||||||||||| || || || |||||||||||||| || | || | | | || | | |||| || | | | | | ||| ||| || | ||
TCCAACAAGGCCGAATCCTGCAGCGGGAGGCGAAACGTGTGCAGAGACAGGAATAGGCGTGTTCTTTAGCAAGgtgagtgttccttccgatgcatcgtaatgtggagagataaaaagctcgctgttcacgacgct-----atatccctctatccctgcag-----------------------------------------------------------
upper sequence: LOC_Os08g42600.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G016997_T01 (Zea mays), 5'ss of exon 12
TCCAACAAGACCTAATCCTGCAGCAGGGGGAGAATTATGCGCAGAGACAGGAATAGGTGTATTTTTGAGCAAGgtgagtgtctgaccatactttttgttcaaaaataagtgtctgaccataatttatgttcaaaaataagtgtctgaccttaaagtgccttaatatgcactaaaattcttactgatcgcactgcaatgtttttgtcctgcgcag
|||||||||||| |||||||||||||| || ||| |||||||||||||||||||| ||| || || |||||||||||||| || | |||| || | | | | || || |||||| | | || | | ||
TCCAACAAGACCGAATCCTGCAGCAGGAGGTGAAACATGCGCAGAGACAGGAATAGCTGTGTTCTTTAGCAAGgtgagtgttccttcagatgcattgt---aaggtgaagagataat-atgcttgctgttcactccatatcctatgctcctgcag-----------------------------------------------------------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|58675166|gb|CK063853.1|CK063853EST: GGGGAGAATTATGCGCAGAGACAGGAATAGGTGTATTTTTGAGCAAG ATAGCAAAGCTTGCAGCTATTAGAATCAGAGGTCTTTGTGAAAGGCTGCAA
genomic: GGGGAGAATTATGCGCAGAGACAGGAATAGGTGTATTTTTGAGCAAGgtgagtgtct ... tcctgcgcagATAGCAAAGCTTGCAGCTATTAGAATCAGAGGTCTTTGTGAAAGGCTGCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCCAACAAGACCTAATCCTGCAGCAGGGGGAGAATTATGCGCAGAGACAGGAATAGGTGTATTTTTGAGCAAGgtgagtgtctgaccatactttttgttcaaaaataagtgtctgaccataatttatgttcaaaaataagtgtctgaccttaaagtgccttaatatgcactaaaattcttactgatcgcactgcaatgtttttgtcctgcgcag
- - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG