Transcript: Human XM_017024836.2

PREDICTED: Homo sapiens protein kinase C alpha (PRKCA), transcript variant X1, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
PRKCA (5578)
Length:
3949
CDS:
213..2150

Additional Resources:

NCBI RefSeq record:
XM_017024836.2
NBCI Gene record:
PRKCA (5578)

sgRNA constructs matching this transcript (CRISPRko, NGG PAM)

This list includes CRISPRko constructs with 100% (20mer + NGG) sequence match to the coding regions of this transcript.

Clone ID Target Seq Vector PAM Seq Cut Position Cut % of CDS Length Exon On Target Score[?] Other Matching Genes Orig. Target Gene[?] Notes Addgene[?]
1 BRDN0001145588 AGGAAGGAAACATGGAACTC pXPR_003 AGG 900 46% 8 0.6276 PRKCA PRKCA 75926
2 BRDN0001148197 CCTTGACCGAGTGAAACTCA pXPR_003 CGG 1006 52% 9 -0.1698 PRKCA PRKCA 75924
3 BRDN0001149352 AGGTGGGGCTTCCGTAAGTG pXPR_003 TGG 323 17% 4 -0.3690 PRKCA PRKCA 75925
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shRNA constructs matching this transcript with 100% SDR[?] match

This list includes all shRNAs that have a perfect SDR[?] match to Human XM_017024836.2, regardless of what transcript they were originally designed to target. For example, this list can include shRNAs that were originally designed to target: (i) a different isoform or obsolete version of this transcript (as annotated by NCBI), (ii) a transcript of an orthologous gene (in this collection, generally human-to-mouse or mouse-to-human), or (iii) a transcript of a different gene (from the same or different taxon).

Clone ID Target Seq Vector Match Position Match Region[?] SDR Match %[?] Intrinsic Score[?] Adjusted Score[?] Matches Other Human Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000001691 CGAGCTATTTCAGTCTATCAT pLKO.1 1844 CDS 100% 5.625 4.500 N PRKCA n/a
2 TRCN0000233511 ACCATCCGCTCCACACTAAAT pLKO_005 852 CDS 100% 13.200 9.240 N PRKCA n/a
3 TRCN0000001692 CATGGAACTCAGGCAGAAATT pLKO.1 1106 CDS 100% 13.200 9.240 N PRKCA n/a
4 TRCN0000195322 CGAGGTGAAGGACCACAAATT pLKO.1 308 CDS 100% 13.200 9.240 N PRKCA n/a
5 TRCN0000233514 GAAGATGAAGACGAGCTATTT pLKO_005 1833 CDS 100% 13.200 9.240 N PRKCA n/a
6 TRCN0000196909 GCTGTACTTCGTCATGGAATA pLKO.1 1448 CDS 100% 10.800 7.560 N PRKCA n/a
7 TRCN0000001690 CTTTGGAGTTTCGGAGCTGAT pLKO.1 992 CDS 100% 4.050 2.835 N PRKCA n/a
8 TRCN0000233513 CTGTGGGACTCCAGATTATAT pLKO_005 1706 CDS 100% 15.000 9.000 N PRKCA n/a
9 TRCN0000233512 GGGACCTCATGTACCACATTC pLKO_005 1480 CDS 100% 10.800 6.480 N PRKCA n/a
10 TRCN0000022874 CCTTATGTGAAGCTGAAACTA pLKO.1 792 CDS 100% 5.625 3.938 N Prkca n/a
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shRNA constructs with at least a near match to this transcript

This list includes shRNAs that have at least a >84% (16 of 19 bases) SDR[?] match to the transcript XM_017024836.2, regardless of what transcript they were originally designed to target. For example, this list can include shRNAs that were originally designed to target: (i) a different isoform or obsolete version of this transcript (as annotated by NCBI), (ii) a transcript of an orthologous gene (in this collection, generally human-to-mouse or mouse-to-human), or (iii) a transcript of a different gene (from the same or different taxon). NOTE: this download is a superset of the above result set.

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All ORF constructs matching this transcript

Clone ID DNA Barcode Vector Sequenced %[?] Nuc. Match %[?] Prot. Match %[?] Epitope Tag Match Diffs[?] Addgene[?]
1 ccsbBroadEn_01281 pDONR223 100% 93.3% 92.5% None (many diffs) n/a
2 TRCN0000472511 CAAAGCGAGGGGGAGCATCGCTTC pLX_317 22.4% 93.3% 92.5% V5 (many diffs) n/a
3 ccsbBroad304_01281 pLX_304 33.6% 93.2% 70.2% V5 (not translated due to prior stop codon) (many diffs) n/a
4 TRCN0000489154 CGCAACGTCAAACTGACCTGCCAT pLX_317 20.3% 93.3% 92.5% V5 (not translated due to prior stop codon) (many diffs) n/a
5 ccsbBroadEn_14788 pDONR223 72.5% 92.8% 34.4% None (many diffs) n/a
6 ccsbBroad304_14788 pLX_304 26.3% 92.8% 34.4% V5 (not translated due to prior stop codon) (many diffs) n/a
7 TRCN0000475052 TTCAATCGGTGGGAGACCACTGAG pLX_317 18.9% 92.8% 34.4% V5 (not translated due to prior stop codon) (many diffs) n/a
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