Construct: ORF ccsbBroadEn_10461
Construct Description:
- Construct Type:
- ORF
- Other Identifiers:
- ORF004640.1_s300c1, BRDN0000389840
- DNA Barcode:
- None
- Epitope Tag:
- None
- Notes:
- Early stop codon detected
Originally Annotated References:
- Gene:
- PCDHA6 (56142)
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 | 56142 | PCDHA6 | protocadherin alpha 6 | NM_018909.4 | 99.8% | 99.8% | 1275A>G;1314C>A;2848C>T |
| 2 | human | 56140 | PCDHA8 | protocadherin alpha 8 | NM_018911.3 | 92.2% | 90.4% | (many diffs) |
| 3 | human | 56142 | PCDHA6 | protocadherin alpha 6 | NM_031848.3 | 84.2% | 84% | (many diffs) |
| 4 | human | 56145 | PCDHA3 | protocadherin alpha 3 | NM_018906.3 | 83.1% | 82.4% | (many diffs) |
| 5 | human | 56143 | PCDHA5 | protocadherin alpha 5 | NM_018908.3 | 82.4% | 81.4% | (many diffs) |
| 6 | human | 56137 | PCDHA12 | protocadherin alpha 12 | NM_018903.4 | 82.1% | 80.7% | (many diffs) |
| 7 | human | 56144 | PCDHA4 | protocadherin alpha 4 | NM_018907.4 | 82% | 81.4% | (many diffs) |
| 8 | human | 56147 | PCDHA1 | protocadherin alpha 1 | NM_018900.3 | 81.9% | 80.8% | (many diffs) |
| 9 | human | 56146 | PCDHA2 | protocadherin alpha 2 | NM_018905.3 | 81.7% | 80.8% | (many diffs) |
| 10 | human | 56138 | PCDHA11 | protocadherin alpha 11 | NM_018902.4 | 81.6% | 81% | (many diffs) |
| 11 | human | 9752 | PCDHA9 | protocadherin alpha 9 | NM_031857.1 | 80.7% | 80.1% | (many diffs) |
| 12 | human | 56141 | PCDHA7 | protocadherin alpha 7 | NM_018910.3 | 79.7% | 80.6% | (many diffs) |
| 13 | human | 56140 | PCDHA8 | protocadherin alpha 8 | NM_031856.1 | 77.3% | 74.1% | (many diffs) |
| 14 | human | 56142 | PCDHA6 | protocadherin alpha 6 | NM_031849.3 | 72.1% | 72.1% | (many diffs) |
| 15 | human | 56139 | PCDHA10 | protocadherin alpha 10 | NM_031860.3 | 60.3% | 58.8% | (many diffs) |
| 16 | mouse | 12937 | Pcdha6 | protocadherin alpha 6 | NM_007767.3 | 83.4% | 85% | (many diffs) |
Sequence Information
Note: uppercase bases indicate empirically verified sequence.
- ORF start:
- 66
- ORF end:
- 2913
- ORF length:
- 2847
- Sequence:
-
1 gttcgttgca acaaattgat gagcaatgct tttttataat gccaaCTTTG TACAAAAAAG 61 TTGGCATGGT GTTTACCCCG GAGGATAGAT TGGGAAAGCA ATGTCTGCTC CTCCCGCTTC 121 TGCTCCTCGC AGCCTGGAAG GTGGGGAGCG GCCAGCTCCA CTACTCCGTA CCCGAGGAGG 181 CCAAACACGG CACCTTCGTG GGCCGGATCG CGCAGGACCT GGGGCTGGAG CTGGCGGAGC 241 TGGTGCCGCG CCTGTTCAGG ATGGCCTCCA AAGACCGCGA GGACCTTCTG GAGGTAAATC 301 TGCAGAATGG CATTTTGTTT GTGAATTCTC GGATCGACCG CGAGGAGCTG TGCGGGCGGA 361 GCGCGGAGTG CAGCATCCAC CTGGAGGTGA TCGTGGACAG GCCGCTGCAG GTTTTCCATG 421 TGGACGTGGA GGTGAGGGAC ATTAACGACA ACCCGCCCTT GTTCCCGGTA GAGGAACAAA 481 GAGTGCTGAT TTACGAATCT AGGCTGCCAG ATTCTGTGTT TCCACTGGAG GGCGCGTCCG 541 ATGCAGATGT TGGCTCAAAT TCCATCTTAA CCTATAAACT CAGTTCTAGC GAATACTTCG 601 GGCTAGATGT GAAAATAAAC AGTGATGACA ATAAACAAAT TGGGCTCTTA TTAAAGAAAT 661 CCTTGGACAG AGAGGAAGCT CCTGCACACA ACTTATTCCT GACAGCCACA GATGGGGGCA 721 AACCTGAGCT CACAGGCACT GTTCAGCTGC TGGTCACAGT GCTGGATGTG AATGATAATG 781 CTCCCACTTT CGAACAGTCT GAATACGAAG TAAGAATATT CGAAAATGCA GACAACGGAA 841 CAACAGTTAT CAGACTGAAT GCTTCTGATC GGGATGAAGG AGCGAATGGG GCAATTTCAT 901 ATTCTTTTAA TAGCCTTGTT GCAGCCATGG TTATTGACCA CTTTAGCATA GATCGAAATA 961 CGGGAGAAAT AGTGATTCGG GGTAATTTGG ATTTTGAACA AGAAAACTTA TACAAAATCC 1021 TCATTGACGC CACGGACAAA GGCCATCCTC CCATGGCGGG TCATTGCACC GTTTTAGTGA 1081 GAATTTTGGA TAAAAATGAT AACGTCCCTG AGATAGCACT GACTTCCTTA TCCTTGCCTG 1141 TACGTGAAGA CGCTCAATTT GGTACTGTCA TCGCCCTAAT TAGCGTGAAC GACCTCGATT 1201 CAGGTGCCAA CGGGCAGGTG AACTGCTCGC TGACGCCTCA CGTCCCTTTC AAGCTGGTGT 1261 CCACCTTCAA GAATTACTAC TCGTTGGTGC TGGACAGTGC CCTGGACCGC GAGAGCGTGT 1321 CGGCCTATGA GTTGGTGGTG ACCGCGCGGG ACGGGGGCTC GCCTTCGCTG TGGGCCACAG 1381 CCAGCTTGTC TGTGGAGGTG GCCGACATGA ATGACAATGC TCCGGCGTTC GCGCAGCCCG 1441 AGTACACAGT GTTCGTGAAG GAGAACAACC CGCCGGGCTG CCACATCTTC ACGGTGTCTG 1501 CGCGAGACGC GGACGCGCAG GAGAACGCGC TGGTGTCCTA CTCGCTGGTG GAGCGGCGGG 1561 TGGGCGAGCG CGCGTTGTCG AGCTACATTT CGGTGCACGC GGAGAGCGGC AAGGTGTACG 1621 CGCTGCAGCC GCTGGACCAC GAGGAGCTAG AGCTGCTGCA GTTTCAGGTG AGCGCGCGCG 1681 ACGCGGGCGT GCCGCCTCTG GGCAGCAACG TGACGCTGCA GGTGTTCGTG CTGGACGAGA 1741 ACGACAACGC GCCGGCGCTG CTGGCGCCTC GGGTGGGTGG TACTGGTGGT GCAGTGAGCG 1801 AGCTGGTGCC GCGGTCACTG GGTGCAGGCC AAGTGGTGGC GAAGGTGCGC GCAGTTGACG 1861 CCGACTCAGG CTACAACGCG TGGCTTTCGT ATGAGCTGCA GCCCCCGGCA AGCAGCGCTC 1921 GCTTCCCGTT TCGCGTGGGG CTGTACACGG GCGAGATCAG CACCACTCGT GTCCTGGACG 1981 AAGCGGACTC TCCGCGCCAC CGGCTGCTGG TGCTGGTGAA AGACCACGGT GAGCCGGCGC 2041 TGACAGCGAC GGCCACGGTT CTGGTGTCGC TGGTGGAGAG TGGCCAGGCT CCAAAGGCGT 2101 CATCACGGGC GTCGGTGGGC GCCGCGGGCC CAGAGGCGGC GCTGGTGGAT GTCAACGTGT 2161 ACCTGATCAT CGCCATCTGC GCGGTATCCA GCCTGCTGGT CCTCACGCTA CTGCTGTACA 2221 CAGCGCTGCG GTGCTCGGCG CCACCCACCG AGGGCGCGTG CACGGCGGAC AAGCCCACGC 2281 TGGTGTGCTC CAGCGCAGTG GGGAGCTGGT CGTACTCGCA GCAGAGGCGG CAGAGGGTGT 2341 GCTCCGGGGA GGGCCCACCC AAGATGGATC TCATGGCCTT TAGCCCCAGC CTTTCACCTT 2401 GTCCTATTAT GATGGGTAAG GCGGAGAATC AGGATTTAAA TGAAGATCAT GATGCCAAAC 2461 CACGACAGCC CAACCCTGAC TGGCGTTACT CTGCCTCCCT GAGAGCAGGC ATGCACAGCT 2521 CTGTGCACCT AGAGGAGGCT GGCATTCTAC GGGCTGGTCC AGGAGGGCCT GATCAGCAGT 2581 GGCCAACAGT ATCCAGTGCA ACACCAGAAC CAGAGGCAGG AGAAGTGTCC CCTCCAGTCG 2641 GTGCGGGTGT CAACAGCAAC AGCTGGACCT TTAAATACGG ACCAGGCAAC CCCAAACAAT 2701 CCGGTCCCGG TGAGTTGCCC GACAAATTCA TTATCCCAGG ATCTCCTGCA ATCATCTCCA 2761 TCCGGCAGGA GCCTACTAAC AGCCAAATTG ACAAAAGTGA CTTCATAACC TTCGGCAAAA 2821 AGGAGGAGAC CAAGAAAAAG AAGAAAAAGA AGAAGGGTAA CAAGACCCAG GAGAAAAAAG 2881 AGAAAGGGAA CAGCACGACT GACAACAGTG ACTAGAGCCC AACTTTCTTG TACAAAGTtg 2941 gcattataag aaagcattgc ttatcaattt gttgcaacga ac