Sequence
atgc intronic sequence ATGC exonic sequencegtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 10
gtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
|| || | | || || | || ||| | | | || ||| | || | || || ||| | | | ||||| ||| | || || || ||||| ||||| | |||||||||||||||||||| || || | ||||||||||||||||| || || |||||||||
-------gta-tgttcttttccttttttaacttaaatt-agttaagcatcttgttctttgctatttac-tcttctgttttggcagTGGTGATAGAACTCCCAAACAGAAGGTGAAGCTAAAAGTTACTGAGGAAAAACTGCTAAACCTAATGTTGAAATACAATGGAGGCCGACCTAGAGCTGAG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 10
gtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
||| | || | ||| | | | | | | || ||||| | |||| | | || ||| | | | ||||| ||| | || ||||| ||||| ||||| | || |||||||||||||| || ||||| || |||||||||||||||||||| ||| ||| |||||
gtatgttctattccctttttttttatctggtttgt---------taaatgtct-tgttccctatatac-tcttctcttttggcagTGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGGTTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCGAGATCTGAG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 13
gtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtt--tagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
||| | || | ||| | | | || | | || ||||| ||||||| || | || | ||| || ||||| ||| | || ||||| ||||| ||||| | || ||||||||||||| || ||||| || |||||||||||||||||||| ||| ||| |||||
gtatgttctattcccttttt--ttatttggttagt---------taaat----gtgttgtttcctatatactcttctcttttggcagTGGTGATAGAACTCCAAAACAGAAGGTGAAGCTAAAGATTACTGAGGAAAAGCTGCTGAACTTAATGTTGAAATACAATGGTGGCCGGCCTAGATCTGAG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 13
-------gtaaggattactgcctctatgctggttaagctggtat-tgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
||| || | | || | || || || | | || | | | || | | |||| | | || ||| ||||||||| | || || ||||||||||||||| | |||||||| ||||||||||| | || | |||||||| |||||||||||||||||||||||||||
gtatgttgtagcatataat-cacctgttcttcctatccttctctctgtttagtcaggatctgagaagtgttcaactttgttttacatgtc-agTGGCGATAGAACTCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAAAAACTATTAAACCTAATGTTGAAGTACAATGGTGGAAAGCCAAGAGCTGAG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 13
gtaaggattactgcctctatgctggt--taagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
||| | ||| | | || | | | | || || || || | | | ||| ||||| ||| | || || ||||||||||||||| | |||||||| ||||| ||||| | || |||||||||| |||||||| ||||| ||||||||||||
gtatgttttagcatatgatcacctgtcctctcttaactcctctctgttcacccaggccctgagttctg-tttatcttctcttgacagTGGTGATAGAACCCCCAAGCAGAAAGTGAAACTAAAAGTTACAGAGGAGAAACTGTTAAACCTGATGTTGAAGTACAATGGAGGAAAACCAAGAGCTGAG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 12
gtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
||||| || | || | ||| || ||| | ||| || | | | | | ||| || ||||| ||| |||| || || ||||| |||||||||||||| || ||||| || || ||||||||||||| ||||||||||| || | ||| ||| |||||
gtaagatctatgtcatcccatttcttta--cttaaattaagatgtaacctttctctcccagcttagttgtgttttatttgggcagTGGTGATAGGACTCCCAAACAGAAGGTGAAATTGAAAGTCACAGAGGAGAAGCTATTGAATTTGATGTTAAAATACAATGGGGGGAGGCCTAGATCTGAGMapped 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|29674285|gb|CB670560.1|CB670560EST: ACATTTGGGCAGTCAGAAGAATTACGTTCTGTCATTGTTGTGATACGCCA TGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAA
genomic: ACATTTGGGCAGTCAGAAGAATTACGTTCTGTCATTGTTGTGATACGCCAgtaaggatta ... atctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
atctaat putative branch site (score: 3)
tctgttt CT-rich tract
attgaatgataaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggattactgcctctatgctggttaagctggtattgaatgataaatattggtgttgtgtcttgacatctaatatctgtttagTGGCGATCGGACACCAAAGCAGAAAGTGAAATTGAAAGTTACTGAGGAAAAACTCCTGAATTTGATGTTGAAATACAATGGTGGAAAGCCAAGAGCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA