Sequence
atgc intronic sequence ATGC exonic sequenceCGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgccgttctctttggttgccgcggttcaggggttttgttagtggtttggtagtgtttgtggtgctaattggagtgtccctttctgatgtttgctgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47410.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47410.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S93_73V6.1 (Physcomitrella patens), 5'ss of exon 1
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgccgttctctttggttgccgc-ggttcaggggttttgttagtggtttggtagtgtttgtggtgctaattggagt----gtccctttctgat-gtttgctgcag
||| ||||||| || || |||| || ||| ||| | |||||||||||||||||||||||||| |||||||| || || |||||||| || | |||||||| | || | | | | ||| ||||| ||| |||| | | || || ||| ||| || || | ||||| | ||
CGGAGAGATCGGAATAGGGTCGCCTCCCCAGCCCTTCGCTGTCATCTTCGACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttc--tccttgggatggttattaattcctgggttcagttggtggc---gcatcattcatgccgctgtttgtggtcagaaaccgtagctgatcatgtgtc----
upper sequence: LOC_Os01g47410.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S113_31V6.1 (Physcomitrella patens), 5'ss of exon 1
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgccgttctctttggttgccgcggttcaggggttttgttagtggtttggtagtgtttgtggtgctaattggagtgtccctttctgatgtttgctgcag----
||| ||||||| ||| || |||| || ||| || ||||||| || |||||||||||||||||||||||||| || || |||||||| || | |||||||| | | | |||||| || ||||| | | | | | | || ||| ||| ||| | | | | | | || | | |
CGGAGAGATCGGCATTGGGTCGCCTCCTCAGCCTTTTTCCGTCATTTTTGACACCGGGAGCTCCAACCTCTGGGTCCCCTCTGCCAAGTGCTACTTGTCGgtgcgtttc--taattgtggttgt-----tttgtgggttgtctcgattggactgagctactttaggtactagttgtggctttcgtgtgtaatcctgggaaagggggt
upper sequence: LOC_Os01g47410.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ34432 (Selaginella moellendorffii), 5'ss of exon 1
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgcc--gttctctttggttgccgcggttcaggggttttgttagtggtttggtagtgtttgtggt----gctaattggagtgtccctttctgatgtttgctgcag-------------------------------------
|| ||||||| || |||| ||||||||| ||||||| || ||||||||||| ||||||||||| | |||||||||||||| ||| |||| || | | | | |||| ||| | || |||| | | | | | | || || || | | | | |||| | ||| | |
TGGTGAGATCGGGATTGGCAGCCCGCCGCAGGTGTTCACGGTTATCTTCGACACTGGGAGCTCCAATTTGTGGGTGCCTTCCTCGCGATGCATTTTCTCTgtaagtccaaaggtttcttctcttgaaagtgatccttagtttgactggaattattttttttcctggagtctcgactgactagtagttttgcttctagagcttggtttggtgttattattgtcttttactgtttttgtcttctatag
upper sequence: LOC_Os01g47410.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ06917 (Selaginella moellendorffii), 5'ss of exon 1
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgcc--gttctctttggttgccgcggttcaggggttttgttagtggtttggtagtgtttgtggt----gctaattggagtgtccctttctgatgtttgctgcag-------------------------------------
|| ||||| | || |||| ||||||||| ||||||| || ||||||||||| ||||||||||| | |||||||||||||| ||| |||| || | | | | |||| ||| | || |||| | | | | | | || || || | | | | |||| | ||| | |
TGGTGAGATTGGGATTGGCAGCCCGCCGCAGGTGTTCACGGTTATCTTCGACACTGGGAGCTCCAATTTGTGGGTGCCTTCCTCGCGATGCATTTTCTCTgtaagtccaaaggtttcttgtcttgaaagtgatccttagtttgactggaattatttttttacctggagtctcgactgactagtagttttgcttctagcgcttggtttggtgttattattgtcttttactgtttttgtcttctatag
upper sequence: LOC_Os01g47410.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ34433 (Selaginella moellendorffii), 5'ss of exon 1
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgcc--gttctctttggttgccgcggttcaggggttttgttagtggtttggtagtgtttgtggt----gctaattggagtgtccctttctgatgtttgctgcag-------------------------------------
|| ||||| | || |||| ||||||||| ||||||| || ||||||||||| ||||||||||| | |||||||||||||| ||| |||| || | | | | |||| ||| | || |||| | | | | | | || || || | | | | |||| | ||| | |
TGGTGAGATTGGGATTGGCAGCCCGCCGCAGGTGTTCACGGTTATCTTCGACACTGGGAGCTCCAATTTGTGGGTGCCTTCCTCGCGATGCATTTTCTCTgtaagtccaaaggtttcttctcttgaaagtgatccttagtttgactggaattattttttttcctggagtctcgactgactagtagttttgcttctagagcttggtttggtgttattattgtcttttactgtttttgtcttctatag
upper sequence: LOC_Os01g47410.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 1
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgcc--gttctctttggttgcc-gcggttcaggggttttgttagtggtttggtagtgtttgtggtgctaattggagtgtccctttctgatgtttgctgcag
|| ||||| | || |||| ||||||||| ||||||| || ||||||||||| ||||||||||| | |||||||||||||| ||| |||| || | | ||| |||| ||| | | | | | | ||| || ||| || | | | |
TGGTGAGATTGGGATTGGCAGCCCGCCGCAGGTGTTCACGGTTATCTTCGACACTGGGAGCTCCAATTTGTGGGTGCCTTCCTCGCGATGCATTTTCTCTgtaagtccaaagttttcttctcttggaagtgatcctaagttgactttattgtttttgt--cttctatag-------------------------------------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|1631900|gb|C19629.1|C19629EST: ACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCG ATTGCTTGCTACTTCCACTCGAGGTACAAGGCTGGTCAGTCGAGCACGTAT
genomic: ACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgccg ... tttgctgcagATTGCTTGCTACTTCCACTCGAGGTACAAGGCTGGTCAGTCGAGCACGTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGGCGAGATCGCCATCGGCACGCCGCCGCAGATGTTCACCGTCATCTTCGACACCGGGAGCTCCAACCTCTGGGTGCCTTCCTCCAAGTGCCACCTCTCGgtgcgcgccgttctctttggttgccgcggttcaggggttttgttagtggtttggtagtgtttgtggtgctaattggagtgtccctttctgatgtttgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT