Transcript: Mouse XR_001782888.1

PREDICTED: Mus musculus VPS39 HOPS complex subunit (Vps39), transcript variant X2, misc_RNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Vps39 (269338)
Length:
4288
CDS:
(non-coding)

Additional Resources:

NCBI RefSeq record:
XR_001782888.1
NBCI Gene record:
Vps39 (269338)

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_001782888.1, 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 TRCN0000120896 GTTTGAGGTAACACTAGAGAA pLKO.1 342 3UTR 100% 4.950 6.930 N Vps39 n/a
2 TRCN0000345308 GTTTGAGGTAACACTAGAGAA pLKO_005 342 3UTR 100% 4.950 6.930 N Vps39 n/a
3 TRCN0000148592 CCATGTGGTTTCCCAGTTTAA pLKO.1 399 3UTR 100% 13.200 9.240 N VPS39 n/a
4 TRCN0000146521 CCAGCAAACACTCAGATCAAT pLKO.1 2565 3UTR 100% 5.625 3.938 N VPS39 n/a
5 TRCN0000120895 CCACGTCTTGAAGGACACAAA pLKO.1 2321 3UTR 100% 4.950 3.465 N Vps39 n/a
6 TRCN0000345239 CCACGTCTTGAAGGACACAAA pLKO_005 2321 3UTR 100% 4.950 3.465 N Vps39 n/a
7 TRCN0000120892 CGCTGTTATGTTGCAGACAAT pLKO.1 3045 3UTR 100% 4.950 3.465 N Vps39 n/a
8 TRCN0000120894 CGTTGGTTTCAAGAGAGACTA pLKO.1 693 3UTR 100% 4.950 3.465 N Vps39 n/a
9 TRCN0000120893 GCCAGCAAACACTCAGATCAA pLKO.1 2564 3UTR 100% 4.950 3.465 N Vps39 n/a
10 TRCN0000345310 GCCAGCAAACACTCAGATCAA pLKO_005 2564 3UTR 100% 4.950 3.465 N Vps39 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_001782888.1, 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_02753 pDONR223 100% 55.7% None (many diffs) n/a
2 ccsbBroad304_02753 pLX_304 0% 55.7% V5 (many diffs) n/a
3 TRCN0000472102 CAATCTACATGATTAGCGGGCTCA pLX_317 19.4% 55.7% V5 (many diffs) n/a
4 ccsbBroadEn_11723 pDONR223 100% 45.6% None (many diffs) n/a
5 ccsbBroad304_11723 pLX_304 0% 45.6% V5 (many diffs) n/a
6 TRCN0000480144 GCATTGTCAAAAATGCGGCATATC pLX_317 17.6% 45.6% V5 (many diffs) n/a
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