Transcript: Mouse XR_379863.3

PREDICTED: Mus musculus upstream binding protein 1 (Ubp1), transcript variant X4, misc_RNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Ubp1 (22221)
Length:
3725
CDS:
(non-coding)

Additional Resources:

NCBI RefSeq record:
XR_379863.3
NBCI Gene record:
Ubp1 (22221)

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_379863.3, 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 TRCN0000086552 CGATGGAATTCGGCTCTATAA pLKO.1 1494 3UTR 100% 0.000 0.000 N Ubp1 n/a
2 TRCN0000301999 CGATGGAATTCGGCTCTATAA pLKO_005 1494 3UTR 100% 0.000 0.000 N Ubp1 n/a
3 TRCN0000086548 CGGACTGAACTCTATCCAGTA pLKO.1 1916 3UTR 100% 4.050 3.240 N Ubp1 n/a
4 TRCN0000302000 CGGACTGAACTCTATCCAGTA pLKO_005 1916 3UTR 100% 4.050 3.240 N Ubp1 n/a
5 TRCN0000086551 CCCACTGGTATCCACATTCTT pLKO.1 1759 3UTR 100% 5.625 3.938 N Ubp1 n/a
6 TRCN0000331529 CCCACTGGTATCCACATTCTT pLKO_005 1759 3UTR 100% 5.625 3.938 N Ubp1 n/a
7 TRCN0000086549 CGACTTATTAAAGCTGACAAA pLKO.1 1443 3UTR 100% 4.950 3.465 N Ubp1 n/a
8 TRCN0000086550 GCCCTCCGTTTATCATGCAAT pLKO.1 1641 3UTR 100% 4.950 3.465 N Ubp1 n/a
9 TRCN0000302001 GCCCTCCGTTTATCATGCAAT pLKO_005 1641 3UTR 100% 4.950 3.465 N Ubp1 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_379863.3, 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

No results found.