Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgccaattgatttgcttatatattcagggttttcctgtctctggtgcttctttgctattgaaactaaggctgctttcattcatctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAAGCTACAGAATCTTGTTCAGCTGAGGTTGGACAGAAATAGACTGAAAGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g58700.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g58700.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G119759_T04 (Zea mays), 3'ss of exon 3
gtaagatgccaattgatttgcttatatattcagggttttcctgtctctggtgct-tctttgctattgaaactaagg------ctgc-tttcattcatctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAAGCTACAGAATCTTGTTCAGCTGAGGTTGGACAGAAATAGACTGAAAGGA
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gtaag-tcccatttgtattattttttcatttgtaactatttattgtttgacatcatctttggtatctaaacaaaaaaaagacttatgttttatccatctcatgtagAAATTTCCATTCCAATGGGTTGACTGGGAATATACCGTCGGAGCTGGGAAAATTACAGAATCTCGTCGAACTTAGGTTGGATAGGAATAGATTGAAGGGA
upper sequence: LOC_Os04g58700.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G02690.1 (Glycine max), 3'ss of exon 4
gtaagatgccaattgatttgcttatatattcagggttttcctgtctctggtgcttctttgctattgaaactaaggctgctttcattcatctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAAGCTACAGAATCTTGTTCAGCTGAGGTTGGACAGAAATAGACTGAAAGGA
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gtaaaa-gaaattcagtatggtctt----cccgagtaaataaaattattgaatctcatacttattcaaatt-----tgtttacattc-----ctgtagAAACTTGCAGTCCAATGGGTTGACTGGTAGGCTACCTCCTGAGCTTGGAAACTTGAGATACCTTCAAGAACTTCAGCTGGATAGGAATAGGCTTCAAGGA
upper sequence: LOC_Os04g58700.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G42770.1 (Glycine max), 3'ss of exon 4
----gtaagatgccaattgatttgcttatatattcagggttttcctgtctctggtgcttctttgctattgaaactaaggctgctttcattcatctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAAGCTACAGAATCTTGTTCAGCTGAGGTTGGACAGAAATAGACTGAAAGGA
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gtaaaagaaattcagaatggtcttcttgaacagatcaaattat--tgactctcatacttattcg------------aatttgtttgcattc-----ctgtagAAACTTGCAGTCCAATGGGTTGACTGGTAGGCTACCTCCGGAGCTTGGAAACTTGAGATACCTTCAAGAACTTCGGCTGGATAGGAATAGGCTTCAAGGAMapped 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|58652550|gb|CK041230.1|CK041230EST: ACTGGTCCTATACCTCCTGAGCTGGCTGGATTGAGCAGCGTAAGCGTAAT AAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAA
genomic: ACTGGTCCTATACCTCCTGAGCTGGCTGGATTGAGCAGCGTAAGCGTAATgtaagatgcc ... tctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAA
EST:
gi|58661808|gb|CK050488.1|CK050488EST: ACTGGTCCTATACCTCCTGAGCTGGCTGGATTGAGCAGCGTAAGCGTAAT AAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAA
genomic: ACTGGTCCTATACCTCCTGAGCTGGCTGGATTGAGCAGCGTAAGCGTAATgtaagatgcc ... tctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctggtgcttctttgctattgaaactaaggctgctttcattcatctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAAGCTACAGAATCTTGTTCAGCTGAGGTTGGACAGAAATAGACTGAAAGGA
ttcatct CT-rich tract
tattgaaa TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgccaattgatttgcttatatattcagggttttcctgtctctggtgcttctttgctattgaaactaaggctgctttcattcatctgctgtagAAACTTTCATTCCAATGGGTTGACTGGGAATATACCTTCAGAGCTGGGCAAGCTACAGAATCTTGTTCAGCTGAGGTTGGACAGAAATAGACTGAAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA