Sequence
atgc intronic sequence ATGC exonic sequenceGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAGgtgattcacgaattcatcatctcctttttttagttttatatttccaaggtgttctcgggatatttcatgataaatgcatgaacacatgcatatttctgtgcttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g54640.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g54640.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G004352_T01 (Zea mays), 5'ss of exon 8
GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAGgtgattcacgaattcatcatctcctttttttagttttatat-ttccaaggtgttctcgggatatttcatgataaatgcat--gaacacatgcatatttctgtgcttttag
|||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||| || | || || ||||| |||| | | || ||| | || | | | ||||| || ||| | || || | ||| ||| | | | ||| | ||||| |||
GTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaagagtttatcatgtcctcaat--aattctatttattgccacattttctctatatttttta-gagaattccatctgaagaatttcccgtttgtttgcttgtag
upper sequence: LOC_Os04g54640.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 5'ss of exon 8
GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAGgtgattcacgaattcatcatctcctttttttagttttatatttccaaggtgttctcgggatatttcatgataaatgcatgaa-cacatgcatatttctgtgcttttag
||| || || || ||||||| || || || || ||||| || ||||||||||||| || |||||||| || ||||||||||| |||||||| | | ||| ||| ||| | | | || | | | ||| | | || || | | || | |||| ||| |
GTTGGCGGTTGTAGCAATGGCTGGACTTGCAGCAGAAGGCCTGCAATATGACAAAGTGGTTGGTCAATCTGCCGATCTTTTCACTCTTCAGgtttgttctaacttc--catttccctatcacgaagct---ttccacaaatccaactttgatctataatctcaactccctgcttcccatgttctcttcag---------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|38476935|gb|CF961068.1|CF961068EST: TAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG AGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACA
genomic: TAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAGgtgattcacg ... gtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAGgtgattcacgaattcatcatctcctttttttagttttatatttccaaggtgttctcgggatatttcatgataaatgcatgaacacatgcatatttctgtgcttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT