Transcript: Human NM_001253884.1

Homo sapiens alpha kinase 1 (ALPK1), transcript variant 3, mRNA.

Source:
NCBI, updated 2019-08-06
Taxon:
Homo sapiens (human)
Gene:
ALPK1 (80216)
Length:
5234
CDS:
307..3807

Additional Resources:

NCBI RefSeq record:
NM_001253884.1
NBCI Gene record:
ALPK1 (80216)

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 BRDN0001146035 AGTGCACAGAAGGCTCCATG pXPR_003 GGG 871 25% 10 0.9132 ALPK1 ALPK1 76081
2 BRDN0001146195 GAGCCATCGGACTACAGCAA pXPR_003 TGG 1454 42% 10 0.6027 ALPK1 ALPK1 76082
3 BRDN0001146875 TGCCAGTATACCTAGCGACG pXPR_003 TGG 478 14% 8 0.4345 ALPK1 ALPK1 76084
4 BRDN0001145294 CATCCTCGCTCGGGACTGTG pXPR_003 CGG 76 2% 4 0.2911 ALPK1 ALPK1 76083
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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_001253884.1, 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 TRCN0000358258 GGCCTCCATTGTAGGATATTT pLKO_005 726 CDS 100% 15.000 21.000 N ALPK1 n/a
2 TRCN0000021475 CCCAGGAAACTATTGTCTATT pLKO.1 3152 CDS 100% 13.200 9.240 N ALPK1 n/a
3 TRCN0000368514 TTCGAGTGCAGGTTGGATAAA pLKO_005 1381 CDS 100% 13.200 9.240 N ALPK1 n/a
4 TRCN0000195267 CAAGAGGAATTGATCAGTATC pLKO.1 3875 3UTR 100% 10.800 7.560 N ALPK1 n/a
5 TRCN0000021478 CCATCCACAATACTACTGATT pLKO.1 3406 CDS 100% 4.950 3.465 N ALPK1 n/a
6 TRCN0000196495 GCCAATGATTTGCAAGAGGAA pLKO.1 3863 3UTR 100% 2.640 1.848 N ALPK1 n/a
7 TRCN0000021477 GCCCAGGTGAAGGAACATTTA pLKO.1 1309 CDS 100% 13.200 7.920 N ALPK1 n/a
8 TRCN0000021474 GCATGTGTTGTTTAAGCCATT pLKO.1 4073 3UTR 100% 4.050 2.430 N ALPK1 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_001253884.1, 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 TRCN0000491585 GTTTGTAATAGCTAGATAGAACCT pLX_317 9% 93.7% 92.6% V5 (not translated due to prior stop codon) 0_1ins79;41_42ins155 n/a
2 TRCN0000491666 ACGCCATGAGATTTACAGCCTAGG pLX_317 11.4% 93.6% 92.6% V5 (many diffs) n/a
3 ccsbBroadEn_12685 pDONR223 100% 80.9% 76.6% None (many diffs) n/a
4 ccsbBroad304_12685 pLX_304 0% 80.9% 76.6% V5 (many diffs) n/a
5 TRCN0000475108 ATACCTCAAAACCATGTCACAAAA pLX_317 13.4% 80.9% 76.6% V5 (many diffs) n/a
6 ccsbBroadEn_15166 pDONR223 0% 80.9% 76.6% None (many diffs) n/a
7 ccsbBroad304_15166 pLX_304 0% 80.9% 76.6% V5 (many diffs) n/a
8 TRCN0000473886 GCGGCGGGACCCGACATCCATACG pLX_317 10.2% 80.9% 76.6% V5 (many diffs) n/a
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