Sequence
atgc intronic sequence ATGC exonic sequenceGAGCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttccttccttcttccccaattcttttttcttttcttttttttttttactttgctgtgctcatgtgtactcagattgtatcagctttatctatgaaacgttgctatgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g35170.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g35170.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G054378_T04 (Zea mays), 5'ss of exon 3
GAGCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttccttccttcttccccaattcttttttcttttcttttttttttttactttgctgtgctcatgtgtactcagattgtatcagctttatctatgaaacgttgctatgtag
|||||||||| ||| || |||||||||||||||||||| || ||| |||| || |||||||||||||| |||||||||||| | ||| | ||| ||| |||| |||| |||| | | || | ||| | |||| | || ||| | | ||
GAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCGgtgcg---------------caaatgatacttttatttaattttattttatactggcaatgggttgcttgaaggaggatgttctcag----------ggaatcttgatgtccag
upper sequence: LOC_Os01g35170.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G154087_T02 (Zea mays), 5'ss of exon 3
GAGCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttccttccttcttccccaattcttttttcttttcttttttttttttactttgctgtgctcatgtgtactcagattgtatcagctttatctatgaaacgttgctatgtag
|||||||||| ||| || |||||||||||||||||||| || ||| |||| || |||||||||||||| |||||||||||| | | | || ||| ||| |||| |||| |||| || || | | || | | | | | | | || ||| | | ||
GAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCGgtgcg---------------caagtgctacttttatttaattttattttatactg-gcaatg-----ggttgcttgaa----agaggatgttctcagggaatcttgatgtccag
upper sequence: LOC_Os01g35170.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G154087_T03 (Zea mays), 5'ss of exon 3
GAGCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttccttccttcttccccaattcttttttcttttcttttttttttttactttgctgtgctcatgtgtactcagattgtatcagctttatctatgaaacgttgctatgtag
|||||||||| ||| || |||||||||||||||||||| || ||| |||| || |||||||||||||| |||||||||||| | | || | | ||| || | | || | || ||| | | ||| ||||| | | | || | | | |
GAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCGgtgcgcaagtgctacttttatttaat-tttattttatactggcaatgggttgcttgaaagag----gatgttctcagggaatcttga---tgtccagggagtgggagg------
upper sequence: LOC_Os01g35170.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G054378_T08 (Zea mays), 5'ss of exon 3
GAGCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttccttccttcttccccaattcttttttcttttcttttttttttttactttgctgtgctcatgtgtactcagattgtatcagctttatctatgaaacgttgctatgtag
|||||||||| ||| || |||||||||||||||||||| || ||| |||| || |||||||||||||| |||||||||||| | ||| | ||| ||| |||| |||| |||| | | || | ||| | ||||
GAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCGgtgcg---------------caaatgatacttttatttaattttattttatactggcaatgggttgcttgaaggaggatgttctcag---------------------------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|58693195|gb|CK081882.1|CK081882EST: GGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG GGAGCGGGAGGTTCTTGATTTGGCTTGCCAAGAACTCCGGTGAAAGGCGAA
genomic: GGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttcct ... tgctatgtagGGAGCGGGAGGTTCTTGATTTGGCTTGCCAAGAACTCCGGTGAAAGGCGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCGgtgcgttccttccttcttccccaattcttttttcttttcttttttttttttactttgctgtgctcatgtgtactcagattgtatcagctttatctatgaaacgttgctatgtag
- - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - TGCTGC