Sequence
atgc intronic sequence ATGC exonic sequenceTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc...
Basic information
species | Oryza sativa |
transcript | LOC_Os07g48200.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G158162_T03 (Zea mays), 5'ss of exon 5
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttt-tgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgt-tgttacctcattactgatttatcgtttttgtatcatattccc
|||||||||||| || || || |||| |||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||||| ||| | || | | | | | ||||| ||| | || || | ||||||| || | | || |
TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAGgtaactttaacatctgtttggcttccttttcataatttaaacatgtttttttttattgtatattgccgattgcctgatttgtcttccaaaagttatttgg--
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G172621_T01 (Zea mays), 5'ss of exon 5
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttt-----tttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc
|||||||||||| ||||| || ||||||||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||||| || |||||| || ||| | | || | | ||| | || | | || | | | | | ||| |
TTCAAATTCCACGATTGTTCCATTGTTTGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCTGAGgtaacttcagcatttgtttgggtccctttaag--tatgtttttattatatattgctgatttgccttcaaaaagttgtttggaaagagcatcaaaagcatttg---
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G38490.1 (Glycine max), 5'ss of exon 2
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc--------------------------------------------------------------------------
| || ||||||||||||| | || |||||||||||||| || || || || |||||||| |||||| | ||||| ||||||| | | || | | | || | || || | || | || | || ||| || | | | | || | || | | |||| |
-----------------TGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAGgtatgcctctattaatgaaatatt-tatctcaatcttttagtac--acatgtatatgcagtt--cttttcaataactttttattaaagaaaaatatcatcaccctgtaattgcagcacatttaatatgacaatttgtacctgaatttcaggcttactttcctcctatttcacag
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G31270.1 (Glycine max), 5'ss of exon 1
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc--
|| || ||||| | || || | ||||||||||| | || |||||||| ||||| || || || || |||||||| |||||||||||||| |||||||||||| | | || | || | || ||||||||| | | | | || | | | || | | |
TTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGACGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAGgtattttttggagtttgattttctttgaatttg--------taataaaatctcttcaccatgtaattgctgaacatcatacaaactggcatgtgaattgcag
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G05840.1 (Glycine max), 5'ss of exon 7
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc
|| || ||||| | || || | ||||||||||| | || |||||||||||||| || || || || |||||||| |||||||||||||| ||||||||||| | | || | || | || || | | | ||| | ||||| | | | | || || |
TTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAGgtatttttggagtt-tgattttctttgaatttgtaatatgatctcttcaccctgtaattgctgaa-cattatacaaac-tggcatgtgaattgcag----
upper sequence: LOC_Os07g48200.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G30470.1 (Arabidopsis thaliana), 5'ss of exon 5
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc
|| |||| | |||||| || || |||||||| ||| || ||||||||||| || ||||| || || || ||||| |||||||||||||| |||||| ||| | ||| | ||| | || ||| | |||| || |||| | || |||||| | | || |||| |||
TTTGAATTTGAACATTGTACCTCTCTTTGAGAAAACTCTTAGTGCCAGTGATGCTGGTCGCATTGGTCGTCTAGTTCTTCCAAAAGCCTGTGCAGAGgtaaatttcccatt----cctatggtgatgtcttttcttgtccttgaaatatt----ttgtagagttatgactgatgt-ctgcattggtat-atag----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|58671720|gb|CK060406.1|CK060406EST: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCAGAG GCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAA
genomic: GTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtattttttt ... cattttgtagGCATATTTCCCTCCAATTTCTCAGCCAGAAGGTCGTCCTTTGACAATTCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAGgtatttttttgttcacaaccttttgtggttctgcctcctgttaataaaattttagtgttgttacctcattactgatttatcgtttttgtatcatattccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa