Sequence
atgc intronic sequence ATGC exonic sequenceTATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 3
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaa-tagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtag
|||||||||||||| ||||||||||||||||||||||| || ||||||||| ||||||| |||||||| || ||| |||||||||||||||||||||||||| ||| | || |||| | || | | |||| ||| ||||| || | | | |||||
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTGTATGTTGGTCGAAGGGTTTCTGGTGGTGCTGCTCGCACTGGTCCTGATGCATATGAGgtttgtcacttaaccttttatgaatttgatt-----catttttcccttacataaatccaatc-aattgtaattttttgtag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G164265_T03 (Zea mays), 5'ss of exon 3
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatat-attttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtag
|||||||||||||| ||||||||||||||||||||||| || ||||||||| ||||||| ||||||||| || || |||||||||||||||||||||||||| || | | ||| | |||| || || | | | |||| ||| || | | | | |||||
CATAACTGACAGGAAGTTAGGTAAAGGTGGTTTTGGTCAGGTCTATGTTGGTCGAAGGGTTTCTGGTGGAGCTGCCCGCACTGGTCCTGATGCATATGAGgtttgtcacttacacattttatgaatttgatg----gattttttccttacataaatccattaaatggtaaaatttttgtag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 3
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatatattttgctg--taaatatatccttttcacattaatacaatctaaaa-atgaccctatgtag------------------
|| | || |||||||| ||||| |||||||||||||||||||||||||| | ||| || |||||| || |||| || ||||||||||| |||||| | | | | | | | | | | | ||| | || | |||| | | | | || | | |
TAAGATAGAGAGGAAATTGGGTAAGGGTGGTTTTGGTCAAGTTTATGTTGGCCGGAGGTTAAGTGGTGGCTCTGATCGAACAGGTCCTGATGCGGTTGAGgtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 5'ss of exon 3
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatc--taaaaatgaccctatgtag--------
|| ||||| |||||| | |||||||| || ||||||||||||| ||||||||||||||| |||||| | || | | ||| | |||||| |||||| | | | || || ||| | | | | || | | | | | |||| ||| || ||| |
TAAGACTGAGAGGAAACTCGGTAAAGGAGGCTTTGGTCAAGTTTTTGTTGGTAGAAGGGTGAGTGGTGGCAGCGATAGGATTGGGGCCGATGCAATTGAGgtatattgta-aagaagcatacttgagatttttgagggatacagacgaaagaagtctaatcgttaacaaattaattatttttcttaccag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 3
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgt-ttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaat-gaccctatgtag------
|| || || |||||| | ||||||||||| |||||||||||||||||||| |||||||| |||||| | | || | | ||| | |||||| |||||| || ||||| || | | | | | | | | | | || | | | || |
TAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTGATAGGATTGGAGCAGATGCAATTGAGgtattagaaactaaaaagcttggcaaaaatcatgggggttagttcaaaagagttaaatttttgaagagttaattcttttccatttcag
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 3
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgt-ttgctc-------tctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatg-tag
| | || ||||| |||||||| ||||||||||||||||| |||||||| ||||||||| |||||| ||| | | || || |||||||| |||||| | || | ||| | | | | ||| | || || | |||| || || | || |||| | || ||
CAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTGAAAGAACGGGACCTGATGCGCTTGAGgtactattcaaatttttttaaccatatcaaagttttccaatgat-tagtcacttcagat--atgctatttaaagggattcgcataacagMapped 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|66915500|gb|CX102348.1|CX102348EST: GTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAG GTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCC
genomic: GTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctc ... ccctatgtagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TATAACTGACAGGAAATTAGGTAAAGGTGGTTTTGGTCAAGTTTATGTTGGTAGAAGGGTATCTGGTGGAACTAATCGTACTGGTCCTGATGCATATGAGgtttgctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA