Sequence
atgc intronic sequence ATGC exonic sequenceGGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatgaaatatatcctctcccatgtttctgcatcttagccgtttgtaatttgtgtgctagtacactgtcataagatcaccatctcccatgtttcagatga...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g49010.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g49010.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G876520_T03 (Zea mays), 5'ss of exon 3
GGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatgaaatatatcctctcccatgtttctgcatcttagccgtttg-taatttgtgtgctagtacactgtcataagatcaccatctcccatgtttcagatga-
|| || |||||||| || || |||||||||||||||||||||||||| || || ||||||||||| ||||||||||||||||| |||||||||| || || || | || || ||| | | ||| || || ||| ||| || ||| | | ||
GGTAAACAGAGGTTGCTTTACAGCTTACTTGATGCAATGCAATCTCTAACATCCCAAGCTGTTGTCATTGGTGTGAGTTGCCGCTTGgtatgaactaagcttcatcatatttacttgtat-ttaccaatgaaataaacctcaagcctgtcagttgt-atataattgatttctttttttgtgtgtgtgtg
upper sequence: LOC_Os01g49010.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G25850.1 (Glycine max), 5'ss of exon 9
GGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatgaaatatatcctctcccatgtttctgcatcttagccgtttgtaatttgtgtgctagtacactgtcataagatcaccatctcccat-gtttcagatga--
|| || ||||| |||||||||||||| || |||||||||||||| | || ||||| |||||||| |||| | ||||| || |||| || | ||| | ||| || | | | ||| | | |||| | | | || | | | | || | || ||| |
GGTAAACAGAGATTACTCTATAGCTTGCTAGATGCAATGCAATCAATAACATCACAGGCTGTTGTACTTGGCATTAGTTGTCGTCTGgtgtgtgctttatagttatttcctttttcttatataaac--tttcaagtagatgtga-attttgtcatgtctgaatttctgtatgcgattggttgagaaaaat
upper sequence: LOC_Os01g49010.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G41410.1 (Glycine max), 5'ss of exon 8
GGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatgaaatatatcctctcccatgtttctgcatcttagccgtttgtaatttgtgtgctagtacactgtcataagatcaccatctcccatgtttcagatga--
|| || ||||| |||||||||||||| || |||||||||||||| | || ||||| |||||||| |||| | |||||||| |||| || | | | | | ||||| || | | | | | ||||| | || |||| || || | | || ||| |
GGTAAACAGAGATTACTCTATAGCTTGCTAGATGCAATGCAATCAATAACATCACAGGCTGTTGTACTTGGCATTAGTTGCCGTCTGgtgtgtgcttatagttatttcctttttct-tatataaactttcaagtagttgtgaattttgtca-tgtctgaatttctttcatgcgattagttgagaaaaaa
upper sequence: LOC_Os01g49010.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv01s0011g04400.t01 (Vitis vinifera), 5'ss of exon 8
GGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatg-------aaatatatcctctcccat-gtttctgcatcttagccgtttgtaatttgtgtgctagt-acactgtcataagatcaccatctcccatgtttcagatga
||||| || | ||||| |||||||| | ||||||||||||||| | || |||||||| ||||| |||||||| |||||| || | ||||| | ||| | |||| | | ||| | | | | | ||| |||| | | | | | | |||| | | | || |||
GGGAAACAACGATTACTTTATAGCTTGTTGGATGCAATGCAATCTGTGACGTCACAAGCAGTTGTCATTGGTGTCAGTTGCAGACTAgtatgttgctttggacttattttttccccccatatttgctttgcatttttctttcatt-gtgtcttgattatattcttataaactagagacatgcc-tgtca-------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|218491615|gb|FG954647.1|FG954647EST: TGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTG GATGCAGACCAACTCCTAGAGAAAAGGGTTAGATCCCGGTTCTCTCATAGG
genomic: TGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatgaaata ... tcatttttagGATGCAGACCAACTCCTAGAGAAAAGGGTTAGATCCCGGTTCTCTCATAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGAAGCAGAGGTTACTCTATAGCTTACTTGATGCAATGCAATCTCTCACCTCACAAGCTGTTGTTATTGGTGTGAGTTGCCGATTGgtatgaaatatatcctctcccatgtttctgcatcttagccgtttgtaatttgtgtgctagtacactgtcataagatcaccatctcccatgtttcagatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatctcc