Sequence
atgc intronic sequence ATGC exonic sequenceGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g06200.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G333591_T01 (Zea mays), 5'ss of exon 7
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
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GTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAAgtaat-tattctc--aatgtctgtatctgtaattggtggtttatgggcaatacataattcatgtggccttttgtag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G029735_T01 (Zea mays), 5'ss of exon 4
-----GTACAAAAAAGGCGTAT------ATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
| | || | | ||| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||| ||||||| || | | ||||| ||| | | |||||||| || || | || |||| |||||| ||
ATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAAgtaat-tattctcattgt--ctgtatctataattggtggtttatgggcattacttaattcatgtggccttttgtag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G029735_T01 (Zea mays), 5'ss of exon 4
-----GTACAAAAAAGGCGTAT------ATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
| | || | | ||| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||| ||||||| || | | ||||| ||| | | |||||||| || || | || |||| |||||| ||
ATATGACATCACTAATGTTCTTGAAGGGATAGGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAAgtaat-tattctcattgt--ctgtatctataattggtggtttatgggcattacttaattcatgtggccttttgtag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G052515_T01 (Zea mays), 5'ss of exon 5
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| |||||||| |||||||||||||||| ||||||| || || ||||||||| | | ||||||||| || || | || |||| |||||| ||
GTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAAAAGCTTAAGAACAACATCCGTTGGAAgtaat-tattctc--aatgtctgtatctgtaattggtgttttatgggcattacttaattcatgtggccttttgtag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G829408_T01 (Zea mays), 5'ss of exon 7
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||| ||||||| || || ||||||||| | | |||||||| || || | || |||| |||||| ||
GTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAAgtaat-tattctc--aatgtctgtatctgtaattggtggtttatgggcattacttaattcatgtggccttttgtag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G35850.1 (Glycine max), 5'ss of exon 5
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgta-----atatattctc---tttatatccatatctgtaaattgcattttatgggtatcacatgctt---tatgtctcctttttcag---------
|| ||||| ||| | ||||||||||| |||||||| | ||||| || || || || ||||||||||||||||||| || | ||||||||| | | ||| | ||| | || ||| ||| | |||| ||| | || | || | |||
GTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAgtactgtgacacatttttaatttttcttttatgcatgttccttgaagtttagctatatgtagtactagagcaaaattcttacatcaaaccttatag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G18400.1 (Glycine max), 5'ss of exon 2
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag-------------------
|| ||||| ||| | |||||||| || || ||||| ||||||||||| || || ||||||||||| ||||||||| || | |||||||| | | ||| || | | | || | ||| ||| ||||| | | ||| ||| || | |
GTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAAgtagga--atttctatacacctgtccttgcatatttgttttccgaggtattgaaag-tttgaaactctttactgactcctttgatgattggtcag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G09410.1 (Glycine max), 5'ss of exon 5
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgta-----atatattctc---tttatatccatatctgtaaattgcattttatgggtatcacatgctt---tatgtctcctttttcag----------------
|| ||||| ||| | ||||||||||| |||||||| | ||||| || || || || ||||||||||||||||||| || | ||||||||| | | ||| | ||| | | | ||| ||| | |||| ||| | | | || | |||
GTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAgtactgtgacacatttttaatttttcttttgtgtatgtttcttgaagtttagatatatgtagtattagagcaaaattcttacatcaaaccttgtggaatatag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0080g01110.t01 (Vitis vinifera), 5'ss of exon 5
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgta---atatattctctttatatccatatctgtaaa-ttgcattttatgggtatcacatgcttta-----tgtctcctttttcag--------------------
||||| || ||||||||||||||||| || |||||||||||||| || || || || || |||||| | ||||| | || | |||||||| | ||||||| | | | | | | |||| ||| || | | || | | | | | || || |||
GTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAAgtatgaaaatattctgtcatttactttttatttaaagttgttttgaaatgttaataattacctcaacacgtgaagaattactcaaaagttaattgatttttgtag
upper sequence: LOC_Os12g06200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g02510.t01 (Vitis vinifera), 5'ss of exon 5
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaat----atattctctttatatccatatctgtaaat---tgcattttatgggtatcacatgctttatgtctcctttttcag-----------------------------------------
|| || || ||||| ||||||||||| || ||||| || ||||| || || || || ||||||||||||||||||| ||||| |||||||||| | || | | ||| || | | | | | | | || ||| | | | ||| | | ||| ||
GTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAAgtaatcctgaaatattttatatctctaaaaatttgactgcttttatcttaggtttgagttgagattttagcaagcatttggagaacatgtaactcatctaagcattggttgaatgattgattagMapped 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|58679104|gb|CK067791.1|CK067791EST: ACAATATCCGTTGGAA AGGAATTGATGACTCTCGACCAGGAGAAGTTAGTGATGATATGTCCATCTT
genomic: ACAATATCCGTTGGAAgtaatatatt ... cctttttcagAGGAATTGATGACTCCCGACCAGGAGAAGTTAGTGATGATATGTCCATCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAAgtaatatattctctttatatccatatctgtaaattgcattttatgggtatcacatgctttatgtctcctttttcag
- - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC