Sequence
atgc intronic sequence ATGC exonic sequenceATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAGgttcttcctaatttaacattacattatcttcttataatatttatattcagataagaaaagtcaatgcagagtaatactgtttcatcaacatatttagcgt...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g28060.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G319760_T01 (Zea mays), 5'ss of exon 7
ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAGgttcttcctaatttaacattacattatcttcttataatatttatat--tcagataagaaaagtcaatgcagagtaat--actgtttcatcaacatatttagcgt
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ATGGAAATGGCTTCAAAACTAGCACGATGAGGCTTGGGGCAGATGCTATTGTATTCACATGCACTAAAGATGATAGgttagtcttactttgacattgcctcatttatatattcattttgtggcatcagcaaaaacatattacttgatggaaattggaaacagtattagggtactcc----
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G19100.1 (Arabidopsis thaliana), 5'ss of exon 7
ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGC-ACACAAGATAATAG-
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ATGGAAATGGTTTCAAGACCAGCACAATGAGACTTGGGGCAGATGTCATCGTCTTCAGCCGCCATTCGAAGAACCAgtgagtggtcattgttggttatcctatgcgctaatgttctaacagttttccatccagttatctttctaaacaagcaattgtgctaaattttttctattccatctgactag---
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv14s0066g00870.t01 (Vitis vinifera), 5'ss of exon 7
ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGC-ACACAAGATAATAGgttcttcctaatttaacattacattatcttcttataatatttatattcagataagaaaagtcaatgcagagtaatactgtttcatcaacatatttagcgt--
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ATGGAAATGGGTTCAAGACAAGCACAATGAGACTTGGAGCGGATGTGATTGTATTCAGCCGCCACTTGAAAGAGAGgtcttatcccaat--aattacccattttcttaacatggaacttgt-tctattttcaaaatcttgttaaacacttttttttttttttttgataggcaaaagcac
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv17s0000g08750.t01 (Vitis vinifera), 5'ss of exon 6
ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAGgttcttcctaattta-acattacattatcttct--tataatatttatat-tcagataagaaaagtcaatgcagagtaatactgtttcatcaacatatttagcgt
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ATGGAAATGGCTTCAAGACCAGCTCTATGAGACTTGGAGCAGATGTTATTGTCTTCAGCCGCCACCTGGACAATGGgtatgacttgaatgatatcttctattctcttgtgctgttgaatttatatgttcactgtttataaacaattctaagatgcgat-ttccattagaggatggag---
upper sequence: LOC_Os06g28060.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S54_191V6.1 (Physcomitrella patens), 5'ss of exon 5
------------------ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAGgttcttcctaatttaaca--ttacat-tatcttcttataatatttatattcagataagaaaagtcaatgcag--agtaatactgtttcatcaacatatttagcgt-
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AGACCACCATTGGGCAGTATGGAAATGGTTTCAAGACAAGTACAATGCGATTAGGGGCAGATGTTATTGTATTCACTAGGAATCGAAATTTGAAAACTGGgtaagcggaactgttttcatgtgctttcttttttctgaaatattggaaagtggggagtttttgctgttacagctgaagttatgcaaacttccattatgttMapped 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|29636270|gb|CB641279.1|CB641279EST: ATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAG GAGATTGACACGGAGTATTGGTCTACTCTCTTATACATTCCTTACAAAAAC
genomic: ATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAGgttcttccta ... gttttgacagGAGATTGACACGGAGTATTGGTCTACTCTCTTATACATTCCTTACAAAAAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGGAAATGGGTTCAAAACCAGCACAATGAGACTTGGAGCAGATGTTATTGTATTCAGCTGCACACAAGATAATAGgttcttcctaatttaacattacattatcttcttataatatttatattcagataagaaaagtcaatgcagagtaatactgtttcatcaacatatttagcgt
- - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa