Transcript: Mouse XM_011247169.2

PREDICTED: Mus musculus regulatory factor X, 3 (influences HLA class II expression) (Rfx3), transcript variant X9, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Rfx3 (19726)
Length:
8807
CDS:
789..3038

Additional Resources:

NCBI RefSeq record:
XM_011247169.2
NBCI Gene record:
Rfx3 (19726)

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.

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 XM_011247169.2, 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 TRCN0000232127 GACCCAAGCCATTCGAAATTT pLKO_005 2153 CDS 100% 15.000 21.000 N RFX3 n/a
2 TRCN0000429600 GACCCAAGCCATTCGAAATTT pLKO_005 2153 CDS 100% 15.000 21.000 N Rfx3 n/a
3 TRCN0000412570 AGCTCGGGAGGAACCTATTTG pLKO_005 1176 CDS 100% 13.200 18.480 N Rfx3 n/a
4 TRCN0000084614 GCGAAGATACACATCGCTCAA pLKO.1 2276 CDS 100% 4.050 5.670 N Rfx3 n/a
5 TRCN0000428889 CCATGGTTATCCGGGACTTAA pLKO_005 2605 CDS 100% 13.200 9.240 N Rfx3 n/a
6 TRCN0000431736 TTGGCAGCAGATGCATCAAAT pLKO_005 3475 3UTR 100% 13.200 9.240 N Rfx3 n/a
7 TRCN0000084617 CGTTGTTGTGAATCTTCAGTT pLKO.1 1886 CDS 100% 4.950 3.465 N Rfx3 n/a
8 TRCN0000084615 CCGAACAACAACTTATCCCTA pLKO.1 1004 CDS 100% 2.640 1.848 N Rfx3 n/a
9 TRCN0000084616 CGTCACAAGTACACAGACCAT pLKO.1 2975 CDS 100% 2.640 1.848 N Rfx3 n/a
10 TRCN0000084613 CTGAAGGTTGACTGTTGTCAA pLKO.1 3112 3UTR 100% 0.495 0.347 N Rfx3 n/a
11 TRCN0000166364 CACACACACACACACACACAA pLKO.1 4694 3UTR 100% 4.950 2.475 Y KAAG1 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_011247169.2, 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_01393 pDONR223 100% 92.4% 98.9% None (many diffs) n/a
2 ccsbBroad304_01393 pLX_304 0% 92.4% 98.9% V5 (many diffs) n/a
3 ccsbBroadEn_11098 pDONR223 100% 50.8% 52.9% None (many diffs) n/a
4 ccsbBroad304_11098 pLX_304 0% 50.8% 52.9% V5 (many diffs) n/a
5 TRCN0000481511 AACTACTTAATTAAATATAGCAAC pLX_317 36.4% 50.8% 52.9% V5 (many diffs) n/a
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