Transcript: Mouse NM_011584.4

Mus musculus nuclear receptor subfamily 1, group D, member 2 (Nr1d2), mRNA.

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.

shRNA constructs matching this transcript with 100% SDR[?]The SDR or "Specificity-Defining Region" encompasses the 19 bases within the shRNA stem region that are retained during siRNA processing/production. These are thus the bases that define the target specificity of the shRNA. Note that, while our shRNA designs nearly always extend the stem by two additional bases matching the intended target transcript (reported in the "Target Seq" column), these additional bases are not relevant to target specificity. match

This list includes all shRNAs that have a perfect SDR[?]The SDR or "Specificity-Defining Region" encompasses the 19 bases within the shRNA stem region that are retained during siRNA processing/production. These are thus the bases that define the target specificity of the shRNA. Note that, while our shRNA designs nearly always extend the stem by two additional bases matching the intended target transcript (reported in the "Target Seq" column), these additional bases are not relevant to target specificity. match to Mouse NM_011584.4, 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[?]The region of the transcript where the match occurs (5UTR, CDS, 3UTR). NOTE: all matches to non-coding transcripts are labeled 3UTR.	SDR Match %[?]Percent match of the "Specificity-Defining Region" of the hairpin target sequence to transcript RNA sequence. The SDR is defined as the initial 19 bases of the (21mer) target sequence. 84% = 16/19 89% = 17/19 95% = 18/19 100% = 19/19	Intrinsic Score[?]Also called "original score", this assesses the target sequence for predicted cloneability and knockdown performance.	Adjusted Score[?]Also called "specificity score", this is a function of the intrinsic score and the specificity factor.	Matches Other Mouse Gene?[?]Does this construct also match another Mouse gene an equal or better degree?	Orig. Target Gene[?]The gene that this construct was originally designed to target	Addgene[?]Link to this entity's page in the Addgene catalog, if available
1	TRCN0000012067	CCGTGCACTAAGGACCTTAAT	pLKO.1	1870	CDS	100%	13.200	18.480	N	Nr1d2	n/a
2	TRCN0000339127	CCGTGCACTAAGGACCTTAAT	pLKO_005	1870	CDS	100%	13.200	18.480	N	Nr1d2	n/a
3	TRCN0000012063	CGACATTAAGAACCTGCTTTA	pLKO.1	3463	3UTR	100%	10.800	8.640	N	Nr1d2	n/a
4	TRCN0000012065	GCTCAGCTCTATGTTTGAGTT	pLKO.1	1717	CDS	100%	4.950	3.960	N	Nr1d2	n/a
5	TRCN0000339064	GCTCAGCTCTATGTTTGAGTT	pLKO_005	1717	CDS	100%	4.950	3.960	N	Nr1d2	n/a
6	TRCN0000351009	CTAGCGCACATTGCCGATATA	pLKO_005	2320	3UTR	100%	13.200	9.240	N	Nr1d2	n/a
7	TRCN0000365705	TTGCCAGATCTTCGATCTTTA	pLKO_005	1943	CDS	100%	13.200	9.240	N	NR1D2	n/a
8	TRCN0000012066	CCAGTATAAGAAGTGCCTGAA	pLKO.1	685	CDS	100%	4.050	2.835	N	Nr1d2	n/a
9	TRCN0000339125	CCAGTATAAGAAGTGCCTGAA	pLKO_005	685	CDS	100%	4.050	2.835	N	Nr1d2	n/a
10	TRCN0000012064	CGCACAGATTGTCCTGTGAAA	pLKO.1	491	CDS	100%	0.495	0.347	N	Nr1d2	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[?]The SDR or "Specificity-Defining Region" encompasses the 19 bases within the shRNA stem region that are retained during siRNA processing/production. These are thus the bases that define the target specificity of the shRNA. Note that, while our shRNA designs nearly always extend the stem by two additional bases matching the intended target transcript (reported in the "Target Seq" column), these additional bases are not relevant to target specificity. match to the transcript NM_011584.4, 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

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