Construct: ORF ccsbBroadEn_01375
Construct Description:
- Construct Type:
- ORF
- Other Identifiers:
- ORF015817.1_s300c1, BRDN0000389629
- 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_000964.4 | 100% | 100% | |
| 2 | human | 5914 | RARA | retinoic acid receptor alpha | NM_001145301.3 | 100% | 100% | |
| 3 | human | 5914 | RARA | retinoic acid receptor alpha | XM_005257553.1 | 100% | 100% | |
| 4 | human | 5914 | RARA | retinoic acid receptor alpha | XM_005257554.1 | 100% | 100% | |
| 5 | human | 5914 | RARA | retinoic acid receptor alpha | XM_011525095.1 | 100% | 100% | |
| 6 | human | 5914 | RARA | retinoic acid receptor alpha | NM_001024809.4 | 91% | 86% | (many diffs) |
| 7 | human | 5914 | RARA | retinoic acid receptor alpha | XM_005257552.5 | 90.3% | 86.3% | (many diffs) |
| 8 | human | 5914 | RARA | retinoic acid receptor alpha | XM_011525096.1 | 87.3% | 87% | 0_1ins167;3G>C;4_5insCCAGCCA |
| 9 | human | 5914 | RARA | retinoic acid receptor alpha | NM_001145302.3 | 79% | 79% | 178_179ins291 |
| 10 | human | 5914 | RARA | retinoic acid receptor alpha | XM_017024920.2 | 74.2% | 74.2% | 0_1ins357 |
| 11 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_001177302.1 | 91.5% | 98.2% | (many diffs) |
| 12 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_001177303.1 | 91.5% | 98.2% | (many diffs) |
| 13 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_009024.2 | 91.5% | 98.2% | (many diffs) |
| 14 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532592.3 | 91.5% | 98.2% | (many diffs) |
| 15 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532593.2 | 91.5% | 98.2% | (many diffs) |
| 16 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_017314353.1 | 91.5% | 98.2% | (many diffs) |
| 17 | mouse | 19401 | Rara | retinoic acid receptor, alpha | NM_001176528.1 | 83.7% | 84.5% | (many diffs) |
| 18 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532596.2 | 68% | 72.7% | (many diffs) |
| 19 | mouse | 19401 | Rara | retinoic acid receptor, alpha | XM_006532597.2 | 68% | 72.7% | (many diffs) |
Sequence Information
Note: uppercase bases indicate empirically verified sequence.
- ORF start:
- 66
- ORF end:
- 1452
- ORF length:
- 1386
- Sequence:
-
1 gttcgttgca acaaattgat gagcaatgct tttttataat gccaaCTTTG TACAAAAAAG 61 TTGGCATGGC CAGCAACAGC AGCTCCTGCC CGACACCTGG GGGCGGGCAC CTCAATGGGT 121 ACCCGGTGCC TCCCTACGCC TTCTTCTTCC CCCCTATGCT GGGTGGACTC TCCCCGCCAG 181 GCGCTCTGAC CACTCTCCAG CACCAGCTTC CAGTTAGTGG ATATAGCACA CCATCCCCAG 241 CCACCATTGA GACCCAGAGC AGCAGTTCTG AAGAGATAGT GCCCAGCCCT CCCTCGCCAC 301 CCCCTCTACC CCGCATCTAC AAGCCTTGCT TTGTCTGTCA GGACAAGTCC TCAGGCTACC 361 ACTATGGGGT CAGCGCCTGT GAGGGCTGCA AGGGCTTCTT CCGCCGCAGC ATCCAGAAGA 421 ACATGGTGTA CACGTGTCAC CGGGACAAGA ACTGCATCAT CAACAAGGTG ACCCGGAACC 481 GCTGCCAGTA CTGCCGACTG CAGAAGTGCT TTGAAGTGGG CATGTCCAAG GAGTCTGTGA 541 GAAACGACCG AAACAAGAAG AAGAAGGAGG TGCCCAAGCC CGAGTGCTCT GAGAGCTACA 601 CGCTGACGCC GGAGGTGGGG GAGCTCATTG AGAAGGTGCG CAAAGCGCAC CAGGAAACCT 661 TCCCTGCCCT CTGCCAGCTG GGCAAATACA CTACGAACAA CAGCTCAGAA CAACGTGTCT 721 CTCTGGACAT TGACCTCTGG GACAAGTTCA GTGAACTCTC CACCAAGTGC ATCATTAAGA 781 CTGTGGAGTT CGCCAAGCAG CTGCCCGGCT TCACCACCCT CACCATCGCC GACCAGATCA 841 CCCTCCTCAA GGCTGCCTGC CTGGACATCC TGATCCTGCG GATCTGCACG CGGTACACGC 901 CCGAGCAGGA CACCATGACC TTCTCGGACG GGCTGACCCT GAACCGGACC CAGATGCACA 961 ACGCTGGCTT CGGCCCCCTC ACCGACCTGG TCTTTGCCTT CGCCAACCAG CTGCTGCCCC 1021 TGGAGATGGA TGATGCGGAG ACGGGGCTGC TCAGCGCCAT CTGCCTCATC TGCGGAGACC 1081 GCCAGGACCT GGAGCAGCCG GACCGGGTGG ACATGCTGCA GGAGCCGCTG CTGGAGGCGC 1141 TAAAGGTCTA CGTGCGGAAG CGGAGGCCCA GCCGCCCCCA CATGTTCCCC AAGATGCTAA 1201 TGAAGATTAC TGACCTGCGA AGCATCAGCG CCAAGGGGGC TGAGCGGGTG ATCACGCTGA 1261 AGATGGAGAT CCCGGGCTCC ATGCCGCCTC TCATCCAGGA AATGTTGGAG AACTCAGAGG 1321 GCCTGGACAC TCTGAGCGGA CAGCCGGGGG GTGGGGGGCG GGACGGGGGT GGCCTGGCCC 1381 CCCCGCCAGG CAGCTGTAGC CCCAGCCTCA GCCCCAGCTC CAACAGAAGC AGCCCGGCCA 1441 CCCACTCCCC GTGCCCAACT TTCTTGTACA AAGTtggcat tataagaaag cattgcttat 1501 caatttgttg caacgaac