Transcript: Mouse XR_380966.3

PREDICTED: Mus musculus VPS54 GARP complex subunit (Vps54), transcript variant X2, misc_RNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Vps54 (245944)
Length:
4983
CDS:
(non-coding)

Additional Resources:

NCBI RefSeq record:
XR_380966.3
NBCI Gene record:
Vps54 (245944)

sgRNA constructs matching this transcript (CRISPRko, NGG PAM)

This list includes CRISPRko constructs with 100% (20mer + NGG) sequence match to the exonic sequence of this non-coding transcript.

No results found.

shRNA constructs matching this transcript with 100% SDR[?] match

This list includes all shRNAs that have a perfect SDR[?] match to Mouse XR_380966.3, 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 TRCN0000304090 TATGGTGTCCCACCTTATTTA pLKO_005 4086 3UTR 100% 15.000 21.000 N VPS54 n/a
2 TRCN0000379896 AGCTAAGCTTGTAGCGATAAT pLKO_005 3395 3UTR 100% 13.200 18.480 N Vps54 n/a
3 TRCN0000092070 CCCAGTGGATTGATCTGTTAA pLKO.1 2155 3UTR 100% 13.200 18.480 N Vps54 n/a
4 TRCN0000092072 GCGATAATGGATAGCCTATTT pLKO.1 3408 3UTR 100% 13.200 18.480 N Vps54 n/a
5 TRCN0000092069 GCGGATGGAAAGATTGCTTTA pLKO.1 2946 3UTR 100% 10.800 15.120 N Vps54 n/a
6 TRCN0000092071 GCATTAAATGATCCTACACTA pLKO.1 1047 3UTR 100% 4.950 6.930 N Vps54 n/a
7 TRCN0000380354 CATGATCGAGCTGTCAAATTT pLKO_005 2652 3UTR 100% 15.000 12.000 N Vps54 n/a
8 TRCN0000118365 GCCATGATCGAGCTGTCAAAT pLKO.1 2650 3UTR 100% 13.200 9.240 N VPS54 n/a
9 TRCN0000310642 GCCATGATCGAGCTGTCAAAT pLKO_005 2650 3UTR 100% 13.200 9.240 N VPS54 n/a
10 TRCN0000379927 ACACGAGGGCTGGTTCATAAG pLKO_005 2357 3UTR 100% 10.800 7.560 N Vps54 n/a
11 TRCN0000380186 ATGACCTCTCAACACGAATTG pLKO_005 1524 3UTR 100% 10.800 7.560 N Vps54 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 XR_380966.3, 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_03331 pDONR223 100% 51.9% None (many diffs) n/a
2 ccsbBroad304_03331 pLX_304 0% 51.9% V5 (many diffs) n/a
3 TRCN0000470913 AGCCGTCATCGCTGTTATTTGCGT pLX_317 15.1% 51.9% V5 (many diffs) n/a
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