Sequence
atgc intronic sequence ATGC exonic sequenceGGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagcccacctcgccccccgactccatcgaatgtaatctcgccgtctccacctcggatctgatctgggtgcttgtgtttttttttcctcgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os08g15040.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G147726_T03 (Zea mays), 5'ss of exon 1
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaag-----cccacctcgccccccgactccatcgaatgtaatctcgccgtctccacctcggatctga---tctgggtgcttgtgtttttttttcctcgcag
|||||||| || |||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||||||||| || |||||| ||| || || | ||| | | |||||| | || || | |||| | |||| | | || | ||
GGCATCGTGTTTACGCGGCTCTTCTCGTCGGTCTTCGGTAACCGCGAGGCTCGCATCCTCGTCCTCGGCCTGGACAATGCTGGCAAGACCACCATACTCTgtaagtcgcacccgcccgttccgtcccctctccctcctcgaatctccacaggtcacccgcagatccgcggttctgttccgcgggggttcccgattctgat--
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G147726_T01 (Zea mays), 5'ss of exon 1
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaag---------cccacctcgccccccgactc-catcgaatgtaatctcgccgtctcca---cctcggatctgatctg--ggtgcttgtgtttttttttcctcgcag---------------------
|||||||| || |||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||||||||| || |||||| ||| || |||| | | | |||||| | | | | | || || ||| |||| || | || | | | || | | | || |
GGCATCGTGTTTACGCGGCTCTTCTCGTCGGTCTTCGGTAACCGCGAGGCTCGCATCCTCGTCCTCGGCCTGGACAATGCTGGCAAGACCACCATACTCTgtaagtcgcacccgcccgttccgtcccctctccctcctcgaatctccacaggtcacccgcagatccgcggttctgttccgcgggggttcccgattctgatccttccgggttgtttcggttcgtttcacag
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA13G01270.1 (Glycine max), 5'ss of exon 1
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagc---ccacctcgccccccgactccatcga-atgtaatctcg-ccgtctccacctcggatctgatctgggtgcttgtgtttttttttcctcgcag
|| | || || || | || || || | ||||| ||| || || || |||||||| ||||||||||||||||||||||| ||||| || || |||| || | ||||| | | |||| || || || | ||| |||| || |||| | | || | || ||| | | |||
GGATTAGTGTTTACCAAATTGTTTTCCTCTCTTTTCGGTAACAAGGAAGCTCGAATCCTCGTTCTCGGCCTCGACAATGCCGGCAAAACCACTATTCTCTgtacgcttcctacctctctgcttctctccctcaccatccgatttgaattttctgtttctcgaat-tgattcgttcgattttattactttc-cttttcag
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA17G07390.1 (Glycine max), 5'ss of exon 1
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagc---ccacctcgcc----ccccgactc--catcgaatgtaatctcgccgtctccacctcggatctgatctgggtgcttgtgtttttttttcctcgcag
|| || || ||||| | || || || | ||||| ||| || || || |||||||| ||||||||||||||||||||||| ||||| || || |||| || | ||||| | | | |||| |||| || | | | || || || ||| || |||| | | || | || || | | |||
GGAATAGTGTTCACCAAATTGTTTTCCTCTCTTTTCGGTAACAAGGAAGCTCGAATCCTCGTTCTCGGCCTCGACAATGCCGGCAAAACCACTATTCTCTgtacgcttcctacctctctgcttctctcactcaccatccgatttgaatttgctgtttc----tcgaatttgattcgttcgattttattaccttc-cttttcag
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT2G24765.1 (Arabidopsis thaliana), 5'ss of exon 1
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagcccac---ctcgccccccgactccatcgaatgta------atctcgccgtctccacctcggatctgatc------tgggt---gcttgtgtttttttttcctcgcag------
|| ||| | ||||||||| | ||||| || ||||| || ||| || || || |||||||||||||| ||||||||||| || || ||||| ||||| ||||| ||| ||| | | | ||| | || | | | | ||| |||| || || | | ||||||| ||| |
GGAATCTTATTCACGCGGATGTTCTCTTCCGTCTTTGGTAACAAAGAAGCTCGAATCCTCGTCCTCGGTCTCGACAATGCTGGAAAAACCACAATCCTCTgtaaattcactgcctcaatctttcgcattgtgtaatagatttgatatttagtagctagggtttttgattcgatcgttttttgagttgcgttgatgtttttgattctctgtgattccag
upper sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ14920 (Selaginella moellendorffii), 5'ss of exon 1
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagcccacctcgcccc-ccgactccatcgaatgtaatctcgccgtctccacctcggatctgatctgggtgcttgtgtttttttttcctcgcag
|| || ||||| | || |||| | || | |||||| | | || ||||| ||||||||||| ||||| ||||| |||||||||||||| || || |||| | ||| || | || | || | || | ||| | || | ||| | | | | |
GGTATGTTCTTCTCTCGATTCTTTACTTCCTTGTTCGGCGATAGGGAAGCCCGGATCCTCGTCCTGGGCCTGGACAACGCCGGCAAGACCACGATTCTCTgtatcctttgatcgatccgtcagatctagcgcttctaggttga--aattccgcggcgatctccgcccgggggtccttaactcgacatttcag---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|88383993|gb|CI631883.1|CI631883EST: CCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTAT ATCGGCTGCAGATGGGGGAGGTCGTCTCCACGATCCCAA
genomic: CCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagcccac ... ttcctcgcagATCGGCTGCAGATGGGGGAGGTCGTCTCCACGATCCCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCATCGTCTTCACGCGGCTCTTCTCGTCGGTCTTCGGCAACCGCGAGGCCCGCATCCTCGTCCTCGGCCTCGACAATGCCGGCAAGACCACCATCCTATgtaagcccacctcgccccccgactccatcgaatgtaatctcgccgtctccacctcggatctgatctgggtgcttgtgtttttttttcctcgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA