Sequence
atgc intronic sequence ATGC exonic sequenceGGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g30800.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g30800.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA08G46570.1 (Glycine max), 5'ss of exon 1
--GGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt---
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TAAGAAAAGATGAATATTTTCAGGTTAGCCGGGGACATGACCCATTTGGCCAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtaccttcctttccaatctcaacat--tcatcgctcgctctgttttgtttcgttgagga-tatgtcgtagattttcattgtaataatgctgacgtgtgt
upper sequence: LOC_Os04g30800.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 5'ss of exon 1
-GGGCGA-GATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgc--ttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt-
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CGATCGAAGATGAACATTTTCAGATTAGCTGGTGATATGACTCACCTAGCCAGTGTTCTTGTCTTGCTTCTCAAGATCCACACCATCAAATCCTGCGCTGgtatgtacat--ttcctcaattcgtttctgaaatttagctgaaatgcgattagattaggctaattctcgat-gtttgttcgatttgcttgacgttgacatttg
upper sequence: LOC_Os04g30800.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
--GGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt
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GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagag--agaaaatt------ttctt------cgattcttttgatttcgtgctgcttagaaatctttgc--gcag------------------
upper sequence: LOC_Os04g30800.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ30337 (Selaginella moellendorffii), 5'ss of exon 1
--GGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt
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GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagag--agaaaatt-----ttcctcga-------ttcttttgatttcgtgctgcttagaaatctttgc--gcag------------------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|88325105|gb|CI646523.1|CI646523EST: GAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTG GTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCT
genomic: GAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgact ... tttcttgtagGTGTTTCCTTGAAAACACAGGAGCTATATGCTCTTGTTTTCGCCACTCGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcgcct