Transcript: Human NM_003992.4

Homo sapiens CDC like kinase 3 (CLK3), transcript variant 2, mRNA.

Source:
NCBI, updated 2019-08-21
Taxon:
Homo sapiens (human)
Gene:
CLK3 (1198)
Length:
1863
CDS:
56..1528

Additional Resources:

NCBI RefSeq record:
NM_003992.4
NBCI Gene record:
CLK3 (1198)

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 BRDN0001146417 AGTCAGACATCAAGACACAC pXPR_003 AGG 656 45% 7 1.0569 CLK3 CLK3 77286
2 BRDN0001147044 ACTGCGATACCCGTCCCGAA pXPR_003 GGG 115 8% 2 0.2758 CLK3 CLK3 77284
3 BRDN0001146636 GAAGAACACCAGCATCCGAG pXPR_003 TGG 949 64% 9 0.246 CLK3 CLK3 77285
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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_003992.4, 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 TRCN0000000748 ACTACTATGGACCTTCACGTT pLKO.1 300 CDS 100% 2.640 3.696 N CLK3 n/a
2 TRCN0000364127 ATGAGGAGGATGTTAGAATTT pLKO_005 1400 CDS 100% 13.200 9.240 N CLK3 n/a
3 TRCN0000000746 CCGTACCAGGAAGCAGAAATA pLKO.1 1252 CDS 100% 13.200 9.240 N CLK3 n/a
4 TRCN0000363092 CTCTGCCACGCCCTTAGATTT pLKO_005 854 CDS 100% 13.200 9.240 N CLK3 n/a
5 TRCN0000195478 CCTTTGGAGAGGACTACTATG pLKO.1 288 CDS 100% 10.800 7.560 N CLK3 n/a
6 TRCN0000363093 GCATTGGCTGCATTCTCTTTG pLKO_005 1131 CDS 100% 10.800 7.560 N CLK3 n/a
7 TRCN0000000749 CATTGGCTGCATTCTCTTTGA pLKO.1 1132 CDS 100% 4.950 3.465 N CLK3 n/a
8 TRCN0000195010 CCTTAGATTTCTGCATGAGAA pLKO.1 865 CDS 100% 4.950 3.465 N CLK3 n/a
9 TRCN0000196581 GCAGAAATATTTCTACAAAGG pLKO.1 1264 CDS 100% 4.050 2.835 N CLK3 n/a
10 TRCN0000196926 GCATTCTCTTTGAGTACTACC pLKO.1 1140 CDS 100% 4.050 2.835 N CLK3 n/a
11 TRCN0000000745 GCTAGAAATCAACGTGCTCAA pLKO.1 652 CDS 100% 4.050 2.835 N CLK3 n/a
12 TRCN0000000747 CCTGTGTGTCTTGATGTCTGA pLKO.1 706 CDS 100% 2.640 1.848 N CLK3 n/a
13 TRCN0000199016 CCACGAAGATCTCGGTCCAGA pLKO.1 185 CDS 100% 0.880 0.616 N CLK3 n/a
14 TRCN0000378182 AGTTTGAAACCCTCTACAATG pLKO_005 939 CDS 100% 10.800 6.480 N CLK3 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_003992.4, 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_00328 pDONR223 100% 100% 100% None n/a
2 ccsbBroad304_00328 pLX_304 0% 100% 100% V5 n/a
3 TRCN0000478370 CCATAGTTGTAAGGTGAAATATGC pLX_317 19.3% 100% 100% V5 n/a
4 ccsbBroadEn_14591 pDONR223 0% 100% 100% None n/a
5 ccsbBroad304_14591 pLX_304 0% 100% 100% V5 n/a
6 TRCN0000475168 TCAGACCTTGCAGATGTCTGTTTT pLX_317 30.3% 100% 100% V5 n/a
7 TRCN0000492252 AGGTTTACCAATGTTAACAAGTCT pLX_317 24.4% 100% 100% V5 (not translated due to prior stop codon) n/a
8 TRCN0000489468 ATGTCCTGTAGTCCGTTCGCAGTC pLX_317 28.1% 100% 100% V5 (not translated due to prior stop codon) n/a
9 TRCN0000489722 CAGTACCAGCGGTACACCAATTTG pLX_317 21% 99.9% 99.7% V5 1470_1471insG n/a
10 TRCN0000488364 AAGTTTTACCAGCTTAGATAGGAT pLX_317 21% 99.9% 99.7% V5 1470_1471insG n/a
11 ccsbBroadEn_06011 pDONR223 100% 99.9% 100% None 1423C>T n/a
12 ccsbBroad304_06011 pLX_304 0% 99.9% 100% V5 1423C>T n/a
13 TRCN0000468038 AAATAGTAAGAAGTATGCTATCGT pLX_317 30.4% 99.9% 100% V5 1423C>T n/a
14 TRCN0000491330 GCCGAGCGGATCGATCCCAGCGGT pLX_317 16.6% 99.4% 100% V5 (not translated due to prior stop codon) 1470_1471insTGAAAGCT n/a
15 ccsbBroadEn_15385 pDONR223 0% 95.3% 95.3% None 470_538del n/a
16 ccsbBroad304_15385 pLX_304 0% 95.3% 95.3% V5 470_538del n/a
17 TRCN0000471198 TTAAGGCGGCTCCGCGGCTTCGAA pLX_317 17.3% 95.3% 95.3% V5 470_538del n/a
18 TRCN0000491339 ATTCTCCCAACGTCGAAGGAAGAG pLX_317 28.2% 95.3% 95.3% V5 (not translated due to prior stop codon) 470_538del n/a
19 TRCN0000489336 TTGTAGAATTCCGGTAAAACAACC pLX_317 25.5% 95.2% 95.1% V5 470_538del;1470_1471insG n/a
20 ccsbBroadEn_15332 pDONR223 100% 11.3% 11.2% None 1_1302del;1456C>T n/a
21 ccsbBroad304_15332 pLX_304 0% 11.3% 11.2% V5 1_1302del;1456C>T n/a
22 TRCN0000480168 GCTTTATGGCAATTGTACTATGTC pLX_317 100% 11.3% 11.2% V5 1_1302del;1456C>T n/a
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