Sequence
atgc intronic sequence ATGC exonic sequence...atgattatactagtaaataccattacaacctcttagcttcaaaggcgtacataattttctttaagaaatattgagctcatcacattatattgtttgctagACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08850.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
atgattatactagtaaataccattacaacctcttagcttcaaaggcgtacataattttctttaagaaatattgagctcatcacattatattgtttgc-tagACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
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ttgattagaataagtagcaatatactatactaatagagtgctcagggtttttttttccttcttaatttgattttgcat-tgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
upper sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0069g00790.t01 (Vitis vinifera), 3'ss of exon 5
atgattatactagtaaataccattacaacctcttagcttcaaaggcgtacataattttctttaagaaatattgagctcatcacat-----tatattgtttgct--agACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
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-----taaactag-atcttctattgcaacctattca-ttctttcttctcttgatttcatttttggtagtttttaccccattccttacttatgttctatttattgcagACCTACTTGCAATCTATCACTGTGAGGCTTGAGGAGTGGAGGCTCAAGCGAAGAGACACAGAGGAATGGATGAGACACCGTCAACTACCTCAAGATCTGC
upper sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0065g00930.t01 (Vitis vinifera), 3'ss of exon 3
--atgat-tatactagtaaataccattacaacctcttagcttcaaaggcgtacataattttctttaagaaatattgagctcatcacattatattgtttgctagACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
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acattatctatcatatgctttattttttccgatccttatctttttatctttcctttatgatttttataattcatgatgct-gtaaagctgttctgat--gtagACATACCTGCAATCTATCACTGTGCGGCTTGAGGAATGGAGACTCAAGCGAAGAGACACTGAGGAATGGATGAGGCATCGCCAACTCCCTGAAGATTTGAMapped 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|29629044|gb|CB634055.1|CB634055EST: TGGCAGTTCTTGGTCTCGTCTTGTTTGCGCATTTGATTGGAAATGTGCAG ACCTACCTGCAATCTATCACTG
genomic: TGGCAGTTCTTGGTCTCGTCTTGTTTGCGCATTTGATTGGAAATGTGCAGgtactttcat ... tgtttgctagACCTACCTGCAATCTATCACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtacataattttctttaagaaatattgagctcatcacattatattgtttgctagACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
ataattttctttaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgattatactagtaaataccattacaacctcttagcttcaaaggcgtacataattttctttaagaaatattgagctcatcacattatattgtttgctagACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA