Sequence
atgc intronic sequence ATGC exonic sequencegtatccttatttccaccactagagttctccagtgttgtgtaaaactatcagtgtcaaatattcttaaaaattcccatttcagGTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTAGAATGCAGACTGGATATTAGCAAGTGTGATTCGAACCAACTTGAAATTC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g02120.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g02120.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G141873_T03 (Zea mays), 3'ss of exon 9
----gtatcctt---atttccacca----ctaga--gttctccagtgttgtgt-aaaactatcagtgtcaaa-----tattcttaaaaattcc-catttcagGTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTAGAATGCAGACTGGATATTAGCAAGTGTGATTCGAACCAACTTGAAATTC
||| |||| || |||| || || || || | | |||||| |||| | ||||| ||| || ||| || ||| |||||||| ||||||| |||| ||||| ||||||||||||||||||||||||||| || |||||| |||||||||||||||| | || ||||||| |||||
gcaggtacccttgccatatccatcaaatttcggactgtcctacttttttgtgttaaaaatgtcagttccaacatacccatgcttgaagatttaatgtttcagGTACAACATGCGTTGGCTCCAGAAGCATCTGACCCTCAACATTCATGGCTGGACTGCAGATTGGATATTAGCAAGTGCAGCCCTAAACAACTTGGAATTC
upper sequence: LOC_Os05g02120.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G141873_T07 (Zea mays), 3'ss of exon 3
gtatcctt---atttccacca----ctaga--gttctccagtgttgtgt-aaaactatcagtgtcaaa-----tattcttaaaaattcc-catttcagGTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTAGAATGCAGACTGGATATTAGCAAGTGTGATTCGAACCAACTTGAAATTC
||| |||| || |||| || || || || | | |||||| |||| | ||||| ||| || ||| || ||| |||||||| ||||||| |||| ||||| ||||||||||||||||||||||||||| || |||||| |||||||||||||||| | || ||||||| |||||
gtacccttgccatatccatcaaatttcggactgtcctacttttttgtgttaaaaatgtcagttccaacatacccatgcttgaagatttaatgtttcagGTACAACATGCGTTGGCTCCAGAAGCATCTGACCCTCAACATTCATGGCTGGACTGCAGATTGGATATTAGCAAGTGCAGCCCTAAACAACTTGGAATTCMapped 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|27548768|gb|CA766627.2|CA766627EST: ACATCATCACCCCAGTATTTGTTCTTAATCCAGCGTATGATGCTTGGCAG GTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTA
genomic: ACATCATCACCCCAGTATTTGTTCTTAATCCAGCGTATGATGCTTGGCAGgtatccttat ... cccatttcagGTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccagtgttgtgtaaaactatcagtgtcaaatattcttaaaaattcccatttcagGTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTAGAATGCAGACTGGATATTAGCAAGTGTGATTCGAACCAACTTGAAATTC
ttcccatttc CT-rich tract
tgtcaaatattcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccttatttccaccactagagttctccagtgttgtgtaaaactatcagtgtcaaatattcttaaaaattcccatttcagGTGCAACATGTGTTGAGTCCAGTAGCATCTGACCCTCAACATTCATGGCTAGAATGCAGACTGGATATTAGCAAGTGTGATTCGAACCAACTTGAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG