Sequence
atgc intronic sequence ATGC exonic sequenceCATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcagggctagctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttccgggttttcctgcacacactactgcttaattattttccc...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37470.3 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 2
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcagggctagctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttccgggttttcctgcacacactactgcttaattattttccc--
||||||||||||||||||||||||||||||||| |||||||||||||||||| |||| ||||||||||| ||||||||||||| |||||||||||||||||| || || | | || | | | || | | | | || | || || | | | || | || | || | |
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTGCTCTACGTCGAGTACCGCACCCGGAAGGAGAAGGAGGGCGTCAGCTTCAGGAACCACGTCATCCAGgtgggtcgg--tcggtcggtcggtcgtcctcctcccccgccgcccagcccacggcgcacgccactcgcccccacctccgcaaccgtttcagacttctttcag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S90_46V6.1 (Physcomitrella patens), 5'ss of exon 2
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcagg-gctagctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttc-cgggttttcctgcac----acactactgcttaattattttccc---------
|| ||| ||||| | ||| | || | | |||||||||||||| || | || || |||| ||| || |||| |||||||||||||||||| |||||| | || | | | | | |||||| ||| | | || ||| | || || | | ||| | | | | |
AATCGGCTGCTGGTCTTGTTACATGATTACCTGGCTCTACGTCGAGTATCGGACGCGGAAAGAGAGGGAGGGGGTCATCTTCAAGAACCACGTCATTCAGgtcctttgaagcaaatagcaaatgaaacttgtagttgcgtcaattttcgcccgtcctgtccaataagttctgttgatttgtaaccttgtttcttgctgaatatggcgatggacag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ18760 (Selaginella moellendorffii), 5'ss of exon 2
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcgg-------cagggctagctcctctccttgcacatcttcgcgtcagtttcagtt--tcgtcag-----tttccgggttttcctgcacacact--actgcttaattattttccc----------------------------------------------------------------------
||||| |||||| ||||| || |||||| |||||| |||||||| || || |||||||| || || |||| |||||||||||| ||||||||||| | | | | || | | |||| | || || | | | || || || | |||| ||| | | | | ||| | | || |
TTTGGGCTCCTGGACTGCCTATCTTATCAGCTGCCTCTATGTCGAGTATCGGGCTCGCAAGGAAAAAGAGAATGTCAACTTCAAGAACCATGTCATCCAGgtagagttatgctaaagtttaaaacttttttcttctttcttttcttctcttctggctgtttgtgagaaggcttggagagtttagctgtagaactttgagagctccaagacttcttccaaagttcctgtagctagaacttcgagagtttgttctcgctgctaaaagagtgatattttttcttgacag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ36050 (Selaginella moellendorffii), 5'ss of exon 2
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcgg-------cagggct--agctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttccggg--ttttcctgcacacact--actgcttaattattttccc----------------------------------------------------------------------
||||| |||||| ||||| || |||||| |||||| |||||||| || || |||||||| || || |||| |||||||||||| ||||||||||| | | | | | | | ||| | ||||| | || | | | | || | | | ||| ||| | | | | ||| | | || |
TTTGGGCTCCTGGACTGCCTATCTTATCAGCTGCCTCTATGTCGAGTATCGGGCTCGCAAGGAAAAAGAGAATGTCAACTTCAAGAACCATGTCATCCAGgtagagttatgctaaagtttaaaacttttttctttcttttcttctcttctggctgtttgtgagaaggcttggagagtttagctgtagaactttgagagctccaagacttcttccaaagttcctgtagctagaacgtcgagagtttgttctcgctgctaaaagagtgatatttgttcttgacag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 2
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcagggctagctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttccgggttttcctg-cacacactactgcttaattattttccc
| || |||||||||||| |||||||| |||||||||||||||||| |||||||||||||| || ||||||||||||||| |||||||||| | | || || | | | | | | | || || || || || || | ||| | | | | | | | || | || |
GCTCGGGGCCTGGACCGCCTATCTCATCAGTTGGCTCTACGTCGAGTACCGCAATCGCAAGGAGAAGGAGAATGTGAGCTTCAAGAACCACATCATCCAGgtaagaa--gcaagaagcaaagatcg-atctttctccatcttttccatcttttccatctttggtgttcttgagtcgcgagcgatggtttctcttgttgcag
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 2
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcag-----ggctagctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttccgggttttcctgcacacactactgcttaattattttccc
| || |||||||||||| ||||||||| |||||||||||||||||| |||||||||||||| || ||||||||||||||| |||||||||| | || || | | || || |||||| | ||| ||| | ||| | | | | | | | | |
GCTCGGGGCCTGGACCGCCTATCTCATCAGCTGGCTCTACGTCGAGTACCGCAATCGCAAGGAGAAGGAGAATGTGAGCTTCAAGAACCACATCATCCAGgtaagaagcaagaagcaaagatcgatctttctccatcttttccaatctttggtgttcttgagtcgcgagcgatggtttctcttgttgcag---------------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|29638464|gb|CB643473.1|CB643473EST: GCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAG TGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGC
genomic: GCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcaggg ... cactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CATGGGCAGCTGGACCGCCTACCTCATCAGCGTCCTCTACGTCGAGTACCGCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcagggctagctcctctccttgcacatcttcgcgtcagtttcagtttcgtcagtttccgggttttcctgcacacactactgcttaattattttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC