Transcript: Mouse XM_006515517.3

PREDICTED: Mus musculus MAP/microtubule affinity regulating kinase 3 (Mark3), transcript variant X6, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Mark3 (17169)
Length:
3395
CDS:
574..2787

Additional Resources:

NCBI RefSeq record:
XM_006515517.3
NBCI Gene record:
Mark3 (17169)

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 BRDN0001146658 ACTGTTGAAAACAATCGGCA pXPR_003 AGG 187 8% 2 -0.0251 Mark3 MARK3 77719
2 BRDN0001145035 TTTGACTATTTGGTTGCACA pXPR_003 TGG 437 20% 6 -0.9134 Mark3 MARK3 77716
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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 Mouse XM_006515517.3, 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 Mouse Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000363374 AGCGGCGAACCGCAACATATA pLKO_005 2237 CDS 100% 13.200 18.480 N Mark3 n/a
2 TRCN0000361306 ACAGGCCGAGAGGTTGCAATA pLKO_005 805 CDS 100% 10.800 15.120 N Mark3 n/a
3 TRCN0000363382 TCTGTTATTAGATGCGGATAT pLKO_005 1122 CDS 100% 10.800 15.120 N Mark3 n/a
4 TRCN0000221201 CGGAAACTACAGACTGTTGAA pLKO.1 732 CDS 100% 4.950 6.930 N Mark3 n/a
5 TRCN0000221202 GCGCTATTCCAGATGAGAGAA pLKO.1 2111 CDS 100% 4.950 6.435 N Mark3 n/a
6 TRCN0000361307 ACCTTAAGGCTAGTTGATAAT pLKO_005 3205 3UTR 100% 13.200 10.560 N Mark3 n/a
7 TRCN0000361259 GAGTAATATTTAGGCAATAAC pLKO_005 2856 3UTR 100% 13.200 10.560 N Mark3 n/a
8 TRCN0000361319 ACCCAGTAATTATGGTGTAAA pLKO_005 2787 CDS 100% 13.200 9.240 N Mark3 n/a
9 TRCN0000361308 CTGAATGGAGTCCGGTTTAAG pLKO_005 2698 CDS 100% 13.200 9.240 N Mark3 n/a
10 TRCN0000355524 GGTGAAGTATTTGACTATTTG pLKO_005 985 CDS 100% 13.200 9.240 N MARK3 n/a
11 TRCN0000378657 TATGGTGGGAATGGGATATTC pLKO_005 1575 CDS 100% 13.200 9.240 N Mark3 n/a
12 TRCN0000221203 CCAAACAGTGACCTCAGCAAT pLKO.1 1690 CDS 100% 4.950 3.465 N Mark3 n/a
13 TRCN0000221200 CGGGAAGTACAGAATCCCTTT pLKO.1 1374 CDS 100% 4.050 2.835 N Mark3 n/a
14 TRCN0000001567 TGAATGAACGAGACACTGAAA pLKO.1 602 CDS 100% 4.950 2.970 N MARK3 n/a
15 TRCN0000378206 ACGCCAATAACTGCGACTATG pLKO_005 2576 CDS 100% 10.800 15.120 N MARK3 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_006515517.3, 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_06560 pDONR223 100% 85% 91.7% None (many diffs) n/a
2 ccsbBroad304_06560 pLX_304 0% 85% 91.7% V5 (many diffs) n/a
3 TRCN0000479389 CTCCATTCAAAATAGAAACCTAGT pLX_317 13.5% 85% 91.7% V5 (many diffs) n/a
4 ccsbBroadEn_14693 pDONR223 0% 85% 91.7% None (many diffs) n/a
5 ccsbBroad304_14693 pLX_304 0% 85% 91.7% V5 (many diffs) n/a
6 TRCN0000474844 TTTGACCTTCCTATAGCGGCACGA pLX_317 3.6% 85% 91.7% V5 (many diffs) n/a
7 TRCN0000488373 AACTGTTCTCACTGAACCGCACCA pLX_317 13.5% 85% 91.7% V5 (not translated due to prior stop codon) (many diffs) n/a
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