Transcript: Human XM_011511347.2

PREDICTED: Homo sapiens pyruvate dehydrogenase kinase 1 (PDK1), transcript variant X13, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
PDK1 (5163)
Length:
4061
CDS:
58..1200

Additional Resources:

NCBI RefSeq record:
XM_011511347.2
NBCI Gene record:
PDK1 (5163)

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 BRDN0001148951 ACCAGGACAGCCAATACAAG pXPR_003 TGG 625 55% 8 -0.1075 PDK1 PDK1 77010
2 BRDN0001145374 CCATCTCATCGAAAACACAT pXPR_003 TGG 476 42% 6 -0.1591 PDK1 PDK1 77008
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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_011511347.2, 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 TRCN0000194672 CATCCGTTCAATTGGTACAAA pLKO.1 143 CDS 100% 5.625 7.875 N PDK1 n/a
2 TRCN0000342424 CATCCGTTCAATTGGTACAAA pLKO_005 143 CDS 100% 5.625 7.875 N PDK1 n/a
3 TRCN0000011007 CGTGAATATGTTGAAGTAGAA pLKO.1 3936 3UTR 100% 4.950 6.930 N PDK1 n/a
4 TRCN0000196891 GCTTAGCTAATCTGACCAAAT pLKO.1 3231 3UTR 100% 10.800 8.640 N PDK1 n/a
5 TRCN0000006262 CCAAACTGCAATGTACTTGAA pLKO.1 550 CDS 100% 4.950 3.960 N PDK1 n/a
6 TRCN0000006260 CGGATCAGAAACCGACACAAT pLKO.1 319 CDS 100% 4.950 3.960 N PDK1 n/a
7 TRCN0000194802 CAGATGCAGTTATCTACATTA pLKO.1 1037 CDS 100% 13.200 9.240 N PDK1 n/a
8 TRCN0000196728 GAAGTAGAAGTCTACCATATT pLKO.1 3948 3UTR 100% 13.200 9.240 N PDK1 n/a
9 TRCN0000342381 GAAGTAGAAGTCTACCATATT pLKO_005 3948 3UTR 100% 13.200 9.240 N PDK1 n/a
10 TRCN0000006261 GCTCTGTCAACAGACTCAATA pLKO.1 1060 CDS 100% 13.200 9.240 N PDK1 n/a
11 TRCN0000342426 GCTCTGTCAACAGACTCAATA pLKO_005 1060 CDS 100% 13.200 9.240 N PDK1 n/a
12 TRCN0000197226 GACTCCCAGTGTATAACAAAG pLKO.1 1085 CDS 100% 10.800 7.560 N PDK1 n/a
13 TRCN0000006263 CCAGGGTGTGATTGAATACAA pLKO.1 360 CDS 100% 5.625 3.938 N PDK1 n/a
14 TRCN0000342425 CCAGGGTGTGATTGAATACAA pLKO_005 360 CDS 100% 5.625 3.938 N PDK1 n/a
15 TRCN0000196635 GATCAGTGAATGCTTGTGAAA pLKO.1 26 5UTR 100% 4.950 3.465 N PDK1 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_011511347.2, 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_01165 pDONR223 100% 78.9% 78.7% None 0_1ins228;183_242del n/a
2 ccsbBroad304_01165 pLX_304 0% 78.9% 78.7% V5 0_1ins228;183_242del n/a
3 TRCN0000479775 CCTTCCAGTTCTCGGGTGCTTTAC pLX_317 11.8% 78.9% 78.7% V5 0_1ins228;183_242del n/a
4 ccsbBroadEn_14737 pDONR223 0% 78.9% 78.7% None 0_1ins228;183_242del n/a
5 ccsbBroad304_14737 pLX_304 0% 78.9% 78.7% V5 0_1ins228;183_242del n/a
6 TRCN0000481546 CCGGTGAGACCGACCATTCAGAAA pLX_317 33.8% 78.9% 78.7% V5 0_1ins228;183_242del n/a
7 TRCN0000488543 ATACCTAATTACACCCTATCTTTA pLX_317 20.4% 78.9% 78.7% V5 0_1ins228;183_242del n/a
8 TRCN0000491614 CTAGCTGAGTGTCGGCTGGCCGCT pLX_317 33.2% 78.9% 78.7% V5 (not translated due to prior stop codon) 0_1ins228;183_242del n/a
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