Sequence
atgc intronic sequence ATGC exonic sequence...tcctggatgcattaattcgtacgtactattaacttactgatgactaatagaattaaattaatctcggttcatctgttctaaatctatctgatctgatcagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g53540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g53540.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37532 (Selaginella moellendorffii), 3'ss of exon 1
tcctggatgcattaattcgtacgtactattaacttactgatgactaatagaattaaattaatctcggttcatctgttctaaatctatctgatctgat--cagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC
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------------------------------------------------gtaagtactgcaagccgagagca--tgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAAT
upper sequence: LOC_Os04g53540.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 2
tcctggatgcattaattcgtacgtactattaacttactgatgactaatagaattaaattaatctcggttcatctgttctaaatctatctgatctgatcagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC
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------------------gtaagagat-tggttttggtgttgttc--tcgattggaagtcctcaaggtggattttttcttcgttt-tct----cgcgcagCTTGTTCAAGGAGTGCCCGCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAAT
upper sequence: LOC_Os04g53540.3 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ34024 (Selaginella moellendorffii), 3'ss of exon 1
tcctggatgcattaattcgtacgtactattaacttactgatgactaatagaattaaattaatctcggttcatctgttctaaatctatctgatctgat--cagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC
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------------------------------------------------gtaagtactacaagccgagagca--tgatgagaacttatctttcttcgtgccagGTTGTTCAAGGAGTGTCCTCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATMapped 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|58671274|gb|CK059960.1|CK059960EST: AAGAAGCGCTACCACCGCCACACCCAGCATCAGATCCAGGAGATGGAAGC ATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAG
genomic: AAGAAGCGCTACCACCGCCACACCCAGCATCAGATCCAGGAGATGGAAGCgtaataacac ... atctgatcagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatagaattaaattaatctcggttcatctgttctaaatctatctgatctgatcagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC
aattaaattaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctggatgcattaattcgtacgtactattaacttactgatgactaatagaattaaattaatctcggttcatctgttctaaatctatctgatctgatcagATTCTTCAAGGAATGTCCACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT