Transcript: Human NM_002610.5

Homo sapiens pyruvate dehydrogenase kinase 1 (PDK1), transcript variant 2, mRNA.

Source:
NCBI, updated 2019-08-27
Taxon:
Homo sapiens (human)
Gene:
PDK1 (5163)
Length:
14072
CDS:
62..1372

Additional Resources:

NCBI RefSeq record:
NM_002610.5
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 BRDN0001149354 AGCGCGCGTAGAAGTCCACC pXPR_003 TGG 137 10% 1 0.6092 PDK1, PDK1-AS1 PDK1 77011
2 BRDN0001147975 TTGCCGCAGAAACATAAATG pXPR_003 AGG 226 17% 2 0.3151 PDK1 PDK1 77009
3 BRDN0001148951 ACCAGGACAGCCAATACAAG pXPR_003 TGG 793 60% 7 -0.0650 PDK1 PDK1 77010
4 BRDN0001145374 CCATCTCATCGAAAACACAT pXPR_003 TGG 644 49% 5 -0.1641 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 NM_002610.5, 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.1 375 CDS 100% 5.625 7.875 N PDK1 n/a
2 TRCN0000342424 CATCCGTTCAATTGGTACAAA pLKO_005 375 CDS 100% 5.625 7.875 N PDK1 n/a
3 TRCN0000011007 CGTGAATATGTTGAAGTAGAA pLKO.1 4108 3UTR 100% 4.950 6.930 N PDK1 n/a
4 TRCN0000196891 GCTTAGCTAATCTGACCAAAT pLKO.1 3403 3UTR 100% 10.800 8.640 N PDK1 n/a
5 TRCN0000006262 CCAAACTGCAATGTACTTGAA pLKO.1 722 CDS 100% 4.950 3.960 N PDK1 n/a
6 TRCN0000006260 CGGATCAGAAACCGACACAAT pLKO.1 491 CDS 100% 4.950 3.960 N PDK1 n/a
7 TRCN0000194802 CAGATGCAGTTATCTACATTA pLKO.1 1209 CDS 100% 13.200 9.240 N PDK1 n/a
8 TRCN0000196728 GAAGTAGAAGTCTACCATATT pLKO.1 4120 3UTR 100% 13.200 9.240 N PDK1 n/a
9 TRCN0000342381 GAAGTAGAAGTCTACCATATT pLKO_005 4120 3UTR 100% 13.200 9.240 N PDK1 n/a
10 TRCN0000006261 GCTCTGTCAACAGACTCAATA pLKO.1 1232 CDS 100% 13.200 9.240 N PDK1 n/a
11 TRCN0000342426 GCTCTGTCAACAGACTCAATA pLKO_005 1232 CDS 100% 13.200 9.240 N PDK1 n/a
12 TRCN0000197226 GACTCCCAGTGTATAACAAAG pLKO.1 1257 CDS 100% 10.800 7.560 N PDK1 n/a
13 TRCN0000006263 CCAGGGTGTGATTGAATACAA pLKO.1 532 CDS 100% 5.625 3.938 N PDK1 n/a
14 TRCN0000342425 CCAGGGTGTGATTGAATACAA pLKO_005 532 CDS 100% 5.625 3.938 N PDK1 n/a
15 TRCN0000196635 GATCAGTGAATGCTTGTGAAA pLKO.1 258 CDS 100% 4.950 3.465 N PDK1 n/a
16 TRCN0000196729 GCACTAAATTTCACTATCTTC pLKO.1 4322 3UTR 100% 4.950 3.465 N PDK1 n/a
17 TRCN0000264189 CAAGTAGCTGGGACTACAGGA pLKO_005 10902 3UTR 100% 2.640 1.320 Y LINC01098 n/a
18 TRCN0000008902 CCTCCCAAAGTGTTGGGATTA pLKO.1 11032 3UTR 100% 1.080 0.540 Y GPR83 n/a
19 TRCN0000156315 CCTCCCAAAGTGTTGGGATTA pLKO.1 11032 3UTR 100% 1.080 0.540 Y MYORG 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 NM_002610.5, 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% 100% 100% None n/a
2 ccsbBroad304_01165 pLX_304 0% 100% 100% V5 n/a
3 TRCN0000479775 CCTTCCAGTTCTCGGGTGCTTTAC pLX_317 11.8% 100% 100% V5 n/a
4 ccsbBroadEn_14737 pDONR223 0% 100% 100% None n/a
5 ccsbBroad304_14737 pLX_304 0% 100% 100% V5 n/a
6 TRCN0000481546 CCGGTGAGACCGACCATTCAGAAA pLX_317 33.8% 100% 100% V5 n/a
7 TRCN0000488543 ATACCTAATTACACCCTATCTTTA pLX_317 20.4% 100% 100% V5 n/a
8 TRCN0000491614 CTAGCTGAGTGTCGGCTGGCCGCT pLX_317 33.2% 100% 100% V5 (not translated due to prior stop codon) n/a
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