Sequence
atgc intronic sequence ATGC exonic sequenceTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgccgagttcttgagacaaacatacatactcttctttttttttttgtaatctttgttcattgagatgtcactgaaattgtaatgcattgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37470.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 3
TTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgccgagttcttgagacaaacatacatactcttctttttttttttgtaatctttgttcattgagatgtcactgaaattgtaatgcattgcag
| || |||||| ||||||||||||||||||||||||| || || ||||||||||| ||||||||||||||| | |||||||||||||||||||| ||||||| || || | ||||| | | ||| ||| | |||| || || | | ||| | | || ||||
TGGACGGGCTCCTGGGCCCGTACTGGAAGGCGGCCGGGCTGGCGTTCAACTGCACGTTCCTGCTCTTCGGCACGGTCATCCAGCTGATCGCCTGCGCAAGgt-gagtca--ggtttctt------------ttctttttcttttctttgcctcccatctctgcatatactagtagagtggcaatggcactggcacgcag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G01240.2 (Arabidopsis thaliana), 5'ss of exon 2
TTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgccgagttcttgagacaaacatacatactcttctttttttttttgtaatctttgttcattgagatgt-cactgaaattgta--atgcattgcag------------------------------
|||||||||| |||| ||||||||||| || || || ||||| || || ||||||||| || | ||||| || ||||||||||| || || ||||| |||| || | || | | | |||| || | | | | || | | | | | | |||| || || ||||
TTGATGGGCTGCTGGGTCCGTACTGGAAAGCAGCGGGGCTCGCATTTAATTGCACCTTCTTGTTATTCGGATCAGTCATCCAGCTCATTGCTTGTGCTAGgtacttcttcctctcttttttattactttttaccaatctttttaatagtatattgatatagagggacaaatacatatatctaaatgataccatcaattgattcatgtgtgtgttgttgttgggatgatgcag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 3
TTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgccgagttcttgagacaaacatacatactcttctttttttttttgtaatctttgttcattgagatgtcact----gaaattgtaatgcattgcag------------------------------
| ||||| | | || || |||||||| ||| || ||| || |||||||||||| ||||||| |||||||| || ||||| ||||||||||| |||| || ||| || | | | | | | | | ||| || || ||| || | | | | | | ||| ||| |
TGGATGGCTTGCTCGGGCCTTACTGGAAAGCGATAGGATTCGGGTTTAACTGCACCTTCTTGCTCTTTGGCTCCGTGATTCAGCTCATCGCCTGTGCGAGgta----cgtcgatatcccagcaaatgccttgctgcggcatctggtgtttgtgggatgtttcctcttctaagttccctttcaaaggactgtttctgatttgaaactcttgggctcgcttgttttctcttgcag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 3
TTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgccgagttcttgagacaaacatacatactcttctttttttttttgtaatctttgttcattgagatgtcact-----gaaattgtaatgcattgcag-----------------------------
| ||||| | | || || |||||||| ||| || ||| || |||||||||||| ||||||| |||||||| || ||||| ||||||||||| |||| || ||| || | | | | | | | | ||| || || | | || | | | | | | | | | || ||| ||
TGGATGGCTTGCTCGGGCCTTACTGGAAAGCGATAGGATTCGGTTTTAACTGCACCTTCTTGCTCTTTGGCTCCGTGATTCAGCTCATCGCCTGTGCGAGgta----cgtcgatatcccagcaaatgccttgctgcggcatctggtgtttgtgggatgtatcctcttctaagttccctttcaaaggactgtttctgatttgaagctcttgggctcgcttgttttctcttgcagMapped 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|29638464|gb|CB643473.1|CB643473EST: TGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAG TAACATATACTACATCAACGACCGGCTGGACAAGAGGACATGGACGTACAT
genomic: TGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgc ... tgcattgcagTAACATATACTACATCAACGACCGGCTGGACAAGAGGACATGGACGTACAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGATCGCCTGTGCAAGgttgactcgccgagttcttgagacaaacatacatactcttctttttttttttgtaatctttgttcattgagatgtcactgaaattgtaatgcattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT