Transcript: Human XM_011542493.3

PREDICTED: Homo sapiens cyclin dependent kinase 11B (CDK11B), transcript variant X4, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
CDK11B (984)
Length:
3642
CDS:
720..3104

Additional Resources:

NCBI RefSeq record:
XM_011542493.3
NBCI Gene record:
CDK11B (984)

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 BRDN0001146011 AAAAGAGAAAAGAGAAACGT pXPR_003 AGG 324 14% 4 0.5669 CDK11B CDK11B 77065
2 BRDN0001146017 CTACATCGTGATGAACTATG pXPR_003 TGG 1549 65% 14 0.311 CDK11B CDK11B 77066
3 BRDN0001146757 ACATCACCGAACGATGAGAG pXPR_003 AGG 652 27% 7 -0.1513 CDK11A, CDK11B CDK11B 77064
4 BRDN0001146432 TCCTTATTGTGATCTCCATG pXPR_003 CGG 173 7% 3 -0.2510 CDK11B CDK11B 77063
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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_011542493.3, 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 TRCN0000197007 GCAGTCAAGAAGATGACCTTC pLKO.1 2724 CDS 100% 4.050 2.835 N CDK11B n/a
2 TRCN0000196705 GAAGTCAGAAATCGATCAGAT pLKO.1 2636 CDS 100% 4.950 2.970 N CDK11B n/a
3 TRCN0000006207 CGATCAGATCAACAAGGTGTT pLKO.1 2648 CDS 100% 4.050 2.430 N CDK11B n/a
4 TRCN0000314694 CGATCAGATCAACAAGGTGTT pLKO_005 2648 CDS 100% 4.050 2.430 N CDK11B n/a
5 TRCN0000314617 ACGGCCTCAAGCATGAGTATT pLKO_005 2863 CDS 100% 13.200 6.600 Y CDK11B n/a
6 TRCN0000380353 AGAGGAGAAAGCAGAGATAAA pLKO_005 797 CDS 100% 13.200 6.600 Y CDK11A n/a
7 TRCN0000380296 AGATGAAATTGTGGCTCTAAA pLKO_005 2096 CDS 100% 13.200 6.600 Y CDK11A n/a
8 TRCN0000006209 CGGCCTCAAGCATGAGTATTT pLKO.1 2864 CDS 100% 13.200 6.600 Y CDK11B n/a
9 TRCN0000196946 GCAGAAGCCAGCACAGTTAAA pLKO.1 1493 CDS 100% 13.200 6.600 Y CDK11B n/a
10 TRCN0000380853 GGCCTCAAGCATGAGTATTTC pLKO_005 2865 CDS 100% 13.200 6.600 Y CDK11A n/a
11 TRCN0000379886 ACTACAGCGACAAAGTGAAAG pLKO_005 1378 CDS 100% 10.800 5.400 Y CDK11A n/a
12 TRCN0000356004 ATGATTCTTTGGCCATCAAAC pLKO_005 958 CDS 100% 10.800 5.400 Y CDK11B n/a
13 TRCN0000356003 CCGCTTGGAGCAGTTAGAAAG pLKO_005 1214 CDS 100% 10.800 5.400 Y CDK11B n/a
14 TRCN0000314695 GAGAGGACTACAGCGACAAAG pLKO_005 1372 CDS 100% 10.800 5.400 Y CDK11B n/a
15 TRCN0000196704 GATGAAATTGTGGCTCTAAAG pLKO.1 2097 CDS 100% 10.800 5.400 Y CDK11B n/a
16 TRCN0000380294 GCCTGATGGAGACCATGAAAC pLKO_005 2290 CDS 100% 10.800 5.400 Y CDK11A n/a
17 TRCN0000380611 GCTGCTTGGTGCCAAGGAATA pLKO_005 2540 CDS 100% 10.800 5.400 Y CDK11A n/a
18 TRCN0000379745 GGAAGCATGCTAGAGTGAAAG pLKO_005 1045 CDS 100% 10.800 5.400 Y CDK11A n/a
19 TRCN0000355952 TCTACATCGTGATGAACTATG pLKO_005 2251 CDS 100% 10.800 5.400 Y CDK11B n/a
20 TRCN0000196539 GATGATTCTTTGGCCATCAAA pLKO.1 957 CDS 100% 5.625 2.813 Y CDK11B n/a
21 TRCN0000006994 CAAGAGGAGAAAGCAGAGATA pLKO.1 795 CDS 100% 4.950 2.475 Y CDK11A n/a
22 TRCN0000006210 CAGATGAAATTGTGGCTCTAA pLKO.1 2095 CDS 100% 4.950 2.475 Y CDK11B n/a
23 TRCN0000197027 GCAGCAACATGGACAAGATCT pLKO.1 2233 CDS 100% 4.950 2.475 Y CDK11A n/a
24 TRCN0000380388 GTGAAGATGAAGAACGAGAAA pLKO_005 1789 CDS 100% 4.950 2.475 Y CDK11A n/a
25 TRCN0000006206 GCCGAAGAAGTAAGTGAGGAA pLKO.1 1761 CDS 100% 2.640 1.320 Y CDK11B n/a
26 TRCN0000006992 CGTATAGAAGAGAAGACTCAA pLKO.1 916 CDS 100% 4.950 2.475 Y CDK11A n/a
27 TRCN0000413041 AGGAAGAAGAGGAGGAGGAAG pLKO_005 1627 CDS 100% 4.050 2.025 Y Myt1 n/a
28 TRCN0000087583 AGGAGGAAGAGGAAGAGGAAA pLKO.1 1696 CDS 100% 4.950 2.475 Y Adam32 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_011542493.3, 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_14570 pDONR223 69.3% 95.2% 63% None (many diffs) n/a
2 ccsbBroad304_14570 pLX_304 0% 95.2% 63% V5 (not translated due to prior stop codon) (many diffs) n/a
3 ccsbBroadEn_13742 pDONR223 100% 49.4% 46.4% None (many diffs) n/a
4 ccsbBroad304_13742 pLX_304 0% 49.4% 46.4% V5 (many diffs) n/a
5 TRCN0000475614 GCGTCAAACGAAAACCATTCTATA pLX_317 10.6% 49.4% 46.4% V5 (many diffs) n/a
6 TRCN0000467626 TAGTGACAATCAACTTACAGCGAA pLX_317 38.1% 35.3% .6% V5 (not translated due to prior stop codon) (many diffs) n/a
7 ccsbBroadEn_14571 pDONR223 100% 35.3% .6% None (many diffs) n/a
8 ccsbBroad304_14571 pLX_304 0% 35.3% .6% V5 (not translated due to prior stop codon) (many diffs) n/a
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