Transcript: Human XM_011545562.2

PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript variant X8, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
RPS6KA3 (6197)
Length:
7694
CDS:
54..2207

Additional Resources:

NCBI RefSeq record:
XM_011545562.2
NBCI Gene record:
RPS6KA3 (6197)

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 BRDN0001144943 ATCACACATCATGTAAAGGA pXPR_003 AGG 83 4% 2 0.7618 RPS6KA3 RPS6KA3 75942
2 BRDN0001148452 AGCTGATGTGCATTAGCACT pXPR_003 AGG 1056 49% 13 0.1762 RPS6KA3 RPS6KA3 75943
3 BRDN0001147852 GGAACGTGATATCTTGGTAG pXPR_003 AGG 280 13% 4 0.14 RPS6KA3 RPS6KA3 75944
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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_011545562.2, 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 TRCN0000194806 CCGTAATTGCTTAGGAGTATT pLKO.1 4495 3UTR 100% 13.200 18.480 N RPS6KA3 n/a
2 TRCN0000427598 GTATTAGGGCAGGGATCATTT pLKO_005 183 CDS 100% 13.200 18.480 N Rps6ka3 n/a
3 TRCN0000196642 GAGATTTGTTTACACGCTTAT pLKO.1 424 CDS 100% 10.800 15.120 N RPS6KA3 n/a
4 TRCN0000295894 GAGATTTGTTTACACGCTTAT pLKO_005 424 CDS 100% 10.800 15.120 N RPS6KA3 n/a
5 TRCN0000001394 CGGCCTAAGTAAAGAGTCTAT pLKO.1 602 CDS 100% 4.950 6.930 N RPS6KA3 n/a
6 TRCN0000194851 CCGGAATCTATTCGAATTTGT pLKO.1 1644 CDS 100% 5.625 4.500 N RPS6KA3 n/a
7 TRCN0000295847 CCGGAATCTATTCGAATTTGT pLKO_005 1644 CDS 100% 5.625 4.500 N RPS6KA3 n/a
8 TRCN0000197173 GCTCAGCGGAGAGGTATTAAA pLKO.1 2163 CDS 100% 15.000 10.500 N RPS6KA3 n/a
9 TRCN0000295893 GCTCAGCGGAGAGGTATTAAA pLKO_005 2163 CDS 100% 15.000 10.500 N RPS6KA3 n/a
10 TRCN0000001397 TCAACGATAGACTGGAATAAA pLKO.1 966 CDS 100% 15.000 10.500 N RPS6KA3 n/a
11 TRCN0000001396 ACTGCCACAATACCAACTAAA pLKO.1 2036 CDS 100% 13.200 9.240 N RPS6KA3 n/a
12 TRCN0000196854 GAAGGGAAGTTGTATCTTATT pLKO.1 384 CDS 100% 13.200 9.240 N RPS6KA3 n/a
13 TRCN0000196545 GATATCTTGGTAGAGGTTAAT pLKO.1 324 CDS 100% 13.200 9.240 N RPS6KA3 n/a
14 TRCN0000040147 GCCTGAAGATACATTCTATTT pLKO.1 1034 CDS 100% 13.200 9.240 N RPS6KA3 n/a
15 TRCN0000288682 GCCTGAAGATACATTCTATTT pLKO_005 1034 CDS 100% 13.200 9.240 N RPS6KA3 n/a
16 TRCN0000194692 CTTTATGCCATGAAGGTATTG pLKO.1 252 CDS 100% 10.800 7.560 N RPS6KA3 n/a
17 TRCN0000001395 CATCCAAACATTATCACTCTA pLKO.1 1401 CDS 100% 4.950 3.465 N RPS6KA3 n/a
18 TRCN0000040146 CTGATGATACACCAGAGGAAA pLKO.1 1849 CDS 100% 4.950 3.465 N RPS6KA3 n/a
19 TRCN0000001398 TCCTACTCTATACAATGCTTA pLKO.1 1801 CDS 100% 4.950 3.465 N RPS6KA3 n/a
20 TRCN0000040143 CCATCTACATAGCCTGGGAAT pLKO.1 512 CDS 100% 4.050 2.835 N RPS6KA3 n/a
21 TRCN0000010429 CAACGATAGACTGGAATAAAC pLKO.1 967 CDS 100% 13.200 7.920 N RPS6KA3 n/a
22 TRCN0000194921 CCTATGAAGTTAGTCCATATA pLKO.1 3005 3UTR 100% 13.200 7.920 N RPS6KA3 n/a
23 TRCN0000010428 CAGAAGAAGATGTCAAATTCT pLKO.1 463 CDS 100% 5.625 3.375 N RPS6KA3 n/a
24 TRCN0000040145 CCCAAAGATTCACCTGGCATT pLKO.1 1080 CDS 100% 4.050 2.430 N RPS6KA3 n/a
25 TRCN0000288683 CCCAAAGATTCACCTGGCATT pLKO_005 1080 CDS 100% 4.050 2.430 N RPS6KA3 n/a
26 TRCN0000423640 ATGGCTCCAGAAGTAGTTAAC pLKO_005 669 CDS 100% 10.800 7.560 N Rps6ka3 n/a
27 TRCN0000138772 GCAGGAGAATCGCTTGAACTT pLKO.1 3872 3UTR 100% 4.950 2.475 Y DCAF11 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_011545562.2, 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_01447 pDONR223 100% 94% 93.3% None (many diffs) n/a
2 ccsbBroad304_01447 pLX_304 0% 94% 93.3% V5 (many diffs) n/a
3 TRCN0000471831 TCGTATTCCCCCACCGAGACCGTA pLX_317 18.6% 94% 93.3% V5 (many diffs) n/a
4 TRCN0000488682 TCCTCACCAGAGTCAACCGTCCAT pLX_317 16.4% 94% 93.3% V5 (not translated due to prior stop codon) (many diffs) n/a
5 ccsbBroadEn_14832 pDONR223 72% 93.6% 24.6% None (many diffs) n/a
6 ccsbBroad304_14832 pLX_304 0% 93.6% 24.6% V5 (not translated due to prior stop codon) (many diffs) n/a
7 TRCN0000473411 AAGCCAAGCGATTACCGCTTACGG pLX_317 15.2% 93.6% 24.6% V5 (not translated due to prior stop codon) (many diffs) n/a
8 ccsbBroadEn_15044 pDONR223 74.3% 75.4% 19.4% None (many diffs) n/a
9 ccsbBroad304_15044 pLX_304 0% 75.4% 19.4% V5 (not translated due to prior stop codon) (many diffs) n/a
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