Sequence
atgc intronic sequence ATGC exonic sequencegtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g14810.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 9
gtgagtaatcaagt--------tgctggttct--agattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
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gtaagtttttatctctcccttataccagttttgtagaagtgtctgtttggcagtcattgcttac--aacacactggaaacttcattaatatccattaattc-tttttactatagGTTATAGTCTCTGCAAGGAAGCCAGAATTTTTCCAGCTTTCACATCCATTGTATGAGGTTGTAACAGATGATGGACTGATGCGTCCCTGTTTTAAAGTAA
upper sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
gtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgat----ttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
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------ggctaaattataaagaat-gcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttg-tgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
upper sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ30141 (Selaginella moellendorffii), 3'ss of exon 9
gtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
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-------------------------------------------------gtaacatacaatg-taccttttttattctgatttctgtccttgggagc-ttacagGTGATTGTGTCAGCGAGAAAGCCAGAGTTTTTCCAAATGTCACATCCCTTGTACGAGATCGTTACCAAGGATGGCTTGATGCGTCCATGTTTCAAAGCAA
upper sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ08324 (Selaginella moellendorffii), 3'ss of exon 9
gtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
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-------------------------------------------------gtaacatacaatg-taccttttttattctgatttctgtccttggaagc-ttacagGTGATTGTGTCCGCGAGAAAGCCAGAGTTTTTCCAAATGTCACATCCCTTGTACGAGATCGTTACCAAGGATGGCTTGATGCGTCCATGTTTCAAAGCAAMapped 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|29627736|gb|CB632747.1|CB632747EST: TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATG GTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
genomic: TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatc ... cttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
EST:
gi|29673384|gb|CB669659.1|CB669659EST: TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATG GTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
genomic: TCAATCGCTTCCTTCCTAATGATATGGCATGGAGAGATCTGTTTGAAATGgtgagtaatc ... cttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
ttcttac putative branch site (score: 2)
tttattctt CT-rich tract
ttgatttattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgatttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA