Construct: ORF ccsbBroadEn_15561
Construct Description:
- Construct Type:
- ORF
- Other Identifiers:
- ORF007102.1_s300c1, BRDN0000390681
- DNA Barcode:
- None
- Epitope Tag:
- None
- Notes:
- No stop codon in insert
Originally Annotated References:
- Gene:
- RARA (5914)
Vector Information:
- Vector Backbone:
- pDONR223
- Pol II Cassette 1:
- n/a
- Pol II Cassette 2:
- n/a
- Selection Marker:
- n/a
- Visible Reporter:
- n/a
- Epitope Tag:
- n/a
Current transcripts matched by this ORF:
| Taxon | Gene | Symbol | Description | Transcript | Nuc. Match %[?]A simple nucleotide-based global alignment percentage, calculated as follows: total nt. matches ---------------------------------- aligned length (incl. gaps) |
Prot. Match %[?]A simple amino acid-based global alignment percentage, calculated as follows: total aa. matches ---------------------------------- aligned length (incl. gaps) |
Match Diffs[?]This field may contain sequence annotations in HGVS format. For more information about HGVS annotations, please refer to the HGVS Quick Reference Guide. | |
|---|---|---|---|---|---|---|---|---|
| 1 | human | 5914 | RARA | retinoic acid receptor alpha | NM_001024809.4 | 100% | 100% | |
| 2 | human | 5914 | RARA | retinoic acid receptor alpha | NM_000964.4 | 91% | 86% | (many diffs) |
| 3 | human | 5914 | RARA | retinoic acid receptor alpha | NM_001145301.3 | 91% | 86% | (many diffs) |
| 4 | human | 5914 | RARA | retinoic acid receptor alpha | XM_005257553.1 | 91% | 86% | (many diffs) |
| 5 | human | 5914 | RARA | retinoic acid receptor alpha | XM_005257554.1 | 91% | 86% | (many diffs) |
| 6 | human | 5914 | RARA | retinoic acid receptor alpha | XM_011525095.1 | 91% | 86% | (many diffs) |
| 7 | human | 5914 | RARA | retinoic acid receptor alpha | XM_005257552.5 | 89.9% | 85.8% | (many diffs) |
| 8 | human | 5914 | RARA | retinoic acid receptor alpha | XM_011525096.1 | 88.3% | 87.9% | 0_1ins148;4_4delCinsGCTCAAACCACT |
| 9 | human | 5914 | RARA | retinoic acid receptor alpha | XM_017024920.2 | 75% | 75% | 0_1ins342 |
| 10 | human | 5914 | RARA | retinoic acid receptor alpha | NM_001145302.3 | 73.2% | 68.6% | (many diffs) |
| 11 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_001176528.1 | 91.4% | 97.6% | (many diffs) |
| 12 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_001177302.1 | 84.1% | 84.6% | (many diffs) |
| 13 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_001177303.1 | 84.1% | 84.6% | (many diffs) |
| 14 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_009024.2 | 84.1% | 84.6% | (many diffs) |
| 15 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532592.3 | 84.1% | 84.6% | (many diffs) |
| 16 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532593.2 | 84.1% | 84.6% | (many diffs) |
| 17 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_017314353.1 | 84.1% | 84.6% | (many diffs) |
| 18 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532596.2 | 68.7% | 73.5% | (many diffs) |
| 19 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532597.2 | 68.7% | 73.5% | (many diffs) |
Sequence Information
Note: uppercase bases indicate empirically verified sequence.
- ORF start:
- 66
- ORF end:
- 1437
- ORF length:
- 1371
- Sequence:
-
1 gttcgttgca acaaattgat gagcaatgct tttttataat gccaactttg tacaaaaaag 61 ttggcatgta cgagagtgta gaagtggggg gtcccacccc taatcccttc ctagtggtgg 121 atttttataa ccagaaccgg gcctgtttgc tcccagagaa ggggctcccc gccccgggtc 181 cgtactccac cccgctccgg actccgcttt ggaatggctc aaaccactcc attgagaccc 241 agagcagcag ttctgaagag atagtgccca gccctccctc gccaccccct ctaccccgca 301 tctacaagcc ttgctttgtc tgtcaggaca agtcctcagg ctaccactat ggggtcagcg 361 cctgtgaggg ctgcaagggc ttcttccgcc gcagcatcca gaagaacatg gtgtacacgt 421 gtcaccggga caagaactgc atcatcaaca aggtgacccg gaaccgctgc cagtactgcc 481 gactgcagaa gtgctttgaa gtgggcatgt ccaaggagtc tgtgagaaac gaccgaaaca 541 agaagaagaa ggaggtgccc aagcccgagt gctctgagag ctacacgctg acgccggagg 601 tgggggagct cattgagaag gtgcgcaaag cgcaccagga aaccttccct gccctctgcc 661 agctgggcaa atacactacg aacaacagct cagaacaacg tgtctctctg gacattgacc 721 tctgggacaa gttcagtgaa ctctccacca agtgcatcat taagactgtg gagttcgcca 781 agcagctgcc cggcttcacc accctcacca tcgccgacca gatcaccctc ctcaaggctg 841 cctgcctgga catcctgatc ctgcggatct gcacgcggta cacgcccgag caggacacca 901 tgaccttctc ggacgggctg accctgaacc ggacccagat gcacaacgct ggcttcggcc 961 ccctcaccga cctggtcttt gccttcgcca accagctgct gcccctggag atggatgatg 1021 cggagacggg gctgctcagc gccatctgcc tcatctgcgg agaccgccag gacctggagc 1081 agccggaccg ggtggacatg ctgcaggagc cgctgctgga ggcgctaaag gtctacgtgc 1141 ggaagcggag gcccagccgc ccccacatgt tccccaagat gctaatgaag attactgacc 1201 tgcgaagcat cagcgccaag ggggctgagc gggtgatcac gctgaagatg gagatcccgg 1261 gctccatgcc gcctctcatc caggaaatgt tggagaactc agagggcctg gacactctga 1321 gcggacagcc ggggggtggg gggcgggacg ggggtggcct ggcccccccg ccaggcagct 1381 gtagccccag cctcagcccc agctccaaca gaagcagccc ggccacccac tccccgtnnc 1441 caactttctt gtacaaagtt ggcattataa gaaagcattg cttatcaatt tgttgcaacg 1501 aac