Sequence
atgc intronic sequence ATGC exonic sequencegtatgctctattttttcttcacttcatcatgcaattacagtggtatcttgtgattatgttctaatttgcaaaacctattacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01010.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G031043_T01 (Zea mays), 3'ss of exon 6
gtatgctctattttttcttcacttcatcatgcaattacagtggtatcttgtgattatgttctaatttgc-------aaaacctat--tacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
||| ||| | | ||| ||||| ||||||| |||||||||| | ||||| || | ||||| | | | |||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||
-------gtatgtttatattcttaattcacacaattgcagtggtctcttgtgattgtattctagttagggataaaaaaaacttttgatgcagTGGTTGATGTGGTGAGAACAGATAGCCACCTTGATTTCTATGGAGAATCAAGGAATATGGCTAGAATGTCTGATATACTTGCTGTTTATGCATGGGTTGA
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G42150.1 (Glycine max), 3'ss of exon 4
--------------------------------------gtatgctctattttttcttcacttcatcatgcaattaca-gtggtatcttgtgattatgttctaatttgcaaaacc--ta--ttacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
| | ||| | | ||| | || | | | | |||| || ||| | ||||| || || || || |||| |||||||| || || || |||||||||||||| ||||| | || | |||||| | ||||||||||||||||| ||||| || ||||||||||||||
gtacctaagttgtatagtgtgtctccctcttcccttctagttaacagagtttatttattctttttgataacagcatatattttatcctgatattct-ttctagcttatggaattattaattttcagTTGTTGATGTTGTGAGGACTGATAGTCATCTTGAATTCTACGAGGACACGAGAAATTTAGCTAGGATGTCAGATATTCTTGCTGTCTATGCATGGGTTGA
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G03240.2 (Glycine max), 3'ss of exon 4
--------------------------------------------gtatgctctattttttcttcacttcatcatgcaattacagtggtatcttgtgattatgttctaatttgcaaaacctattacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
| | ||||| ||||| || || ||| || | | | | || ||||| | | | || |||| |||||||| || || || |||||||||||||| ||||||| || |||||| | ||||||||||||||||| ||||| || ||||||||||||||
gtacctaagttgtatagtgtgtctccctctcccctcctagtttaacagagtttatttattctttttgacaaca-gcatatattttatcctgatattctttctagctaatggggttattatttttcagTTGTTGATGTTGTGAGGACTGATAGTCATCTTGAATTCTATGAGGACAAGAGAAATTTAGCTAGGATGTCAGATATTCTTGCTGTCTATGCATGGGTTGA
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0226g00160.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gtatgctctattttttcttcacttcatcatgcaattacagtggt-atcttgtgattatgttcta-atttgcaaaaccta------ttacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
|||| | | | ||| | |||| | || | | || || | ||| | | || |||| || || |||| |||||||||| ||||| |||||||||||||| ||||||| || ||| |||| |||||||||||||||| || ||||| |||||||||||||||||
gtatatcagtttgtcatttattactttattatgataaaacctagtgaatcttgtttatgccactattggatttatttttgaactattcttcgtgtctgaaaaatcttgttccctttcagTTATTGATGTGGTAAGAACAGATAGTCATCTTGAATTCTATGAGGATCCAAAAAATTTGGCTAGGATGTCAGACATTCTTGCTGTTTATGCATGGGTTGA
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0226g00020.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------gtatgctctatt---ttttcttcacttcatcatgcaattacagtggtatcttgtgattatgttctaatttgcaaaacctattacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
|| ||| | || | | ||| ||| ||||| || | || || || | | || |||| ||||||||||| ||||| |||||||||||||| || |||| || ||| |||| | |||||||||||||| || ||||| |||||||||||||||||
gtaaatcagtttctcatgggtattttattacaataaaacctagcgaatcttgcttatgccataatgggattacctacttaagctactcttttgagctgacagtcctgtttcctttcagTTGTTGATGTGGTAAGAACAGATAGTCATCTTGAATTTTATGAGGATACAAAAAATTTAGCTAGGATGTCAGACATTCTTGCTGTTTATGCATGGGTTGAMapped 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|58689012|gb|CK077699.1|CK077699EST: TGCCAGCAAAGATCGAGTCTCTGAATGGCTTTGGACACTGCACCGAATTG TGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAA
genomic: TGCCAGCAAAGATCGAGTCTCTGAATGGCTTTGGACACTGCACCGAATTGgtatgctcta ... cctattacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcaattacagtggtatcttgtgattatgttctaatttgcaaaacctattacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
ttctaat putative branch site (score: 2)
attatgttctaattt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctctattttttcttcacttcatcatgcaattacagtggtatcttgtgattatgttctaatttgcaaaacctattacagTGGTTGATGTGGTTAGAACGGATAGTCATCTTGATTTCTATGGAGAATCAAGAAATATGGCTAGGATGTCAGATATACTTGCAGTTTATGCATGGGTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG