Transcript: Mouse NM_011664.4

Mus musculus ubiquitin B (Ubb), transcript variant 1, mRNA.

Source:
NCBI, updated 2017-06-26
Taxon:
Mus musculus (mouse)
Gene:
Ubb (22187)
Length:
1513
CDS:
432..1349

Additional Resources:

NCBI RefSeq record:
NM_011664.4
NBCI Gene record:
Ubb (22187)

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 NM_011664.4, 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[?] SDR Match %[?] Intrinsic Score[?] Adjusted Score[?] Matches Other Mouse Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000272013 CCAGTGACACCATCGAGAATG pLKO_005 1171 CDS 100% 10.800 5.400 Y Gm11808 n/a
2 TRCN0000086859 GAAGGCCAAGATCCAGGATAA pLKO.1 509 CDS 100% 10.800 5.400 Y Gm1821 n/a
3 TRCN0000086862 CCGCACCCTCTCTGATTACAA pLKO.1 590 CDS 100% 5.625 2.813 Y Gm1821 n/a
4 TRCN0000098635 CCGCACTCTCTCTGATTACAA pLKO.1 1274 CDS 100% 5.625 2.813 Y Ubb n/a
5 TRCN0000098636 CGAGAATGTGAAGGCCAAGAT pLKO.1 1184 CDS 100% 4.950 2.475 Y Ubb n/a
6 TRCN0000098639 GCACCCTCTCTGATTACAACA pLKO.1 592 CDS 100% 4.950 2.475 Y Ubb n/a
7 TRCN0000086858 CTCTGATTACAACATCCAGAA pLKO.1 599 CDS 100% 4.050 2.025 Y Gm1821 n/a
8 TRCN0000098637 CCTCTCTGATTACAACATCCA pLKO.1 596 CDS 100% 2.640 1.320 Y Ubb n/a
9 TRCN0000098638 CATCGAGAATGTGAAGGCCAA pLKO.1 1181 CDS 100% 2.160 1.080 Y Ubb n/a
10 TRCN0000086861 GATCCAGGATAAAGAGGGCAT pLKO.1 518 CDS 100% 2.160 1.080 Y Gm1821 n/a
11 TRCN0000086860 GCCCAGTGACACCATCGAGAA pLKO.1 485 CDS 100% 1.350 0.675 Y Gm1821 n/a
12 TRCN0000414438 TGAAGACCCTGACCGGCAAGA pLKO_005 673 CDS 100% 1.350 0.675 Y UBB n/a
13 TRCN0000007737 GCCAAGATCCAGGATAAAGAA pLKO.1 513 CDS 100% 5.625 2.813 Y UBB 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 NM_011664.4, 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

Clone ID DNA Barcode Vector Sequenced %[?] Nuc. Match %[?] Prot. Match %[?] Epitope Tag Match Diffs[?] Addgene[?]
1 ccsbBroadEn_14873 pDONR223 70.1% 69.9% 74.7% None (many diffs) n/a
2 ccsbBroad304_14873 pLX_304 0% 69.9% 74.7% V5 (many diffs) n/a
3 ccsbBroadEn_14872 pDONR223 58.4% 69% 74.7% None (many diffs) n/a
4 ccsbBroad304_14872 pLX_304 0% 69% 74.7% V5 (many diffs) n/a
5 TRCN0000468005 TCGGGCCTGTCTTATCTTATATCC pLX_317 100% 23% 24.9% V5 (many diffs) n/a
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