Transcript: Mouse NM_008253.4

Mus musculus high mobility group box 3 (Hmgb3), transcript variant 2, mRNA.

Source:
NCBI, updated 2017-06-04
Taxon:
Mus musculus (mouse)
Gene:
Hmgb3 (15354)
Length:
1751
CDS:
280..882

Additional Resources:

NCBI RefSeq record:
NM_008253.4
NBCI Gene record:
Hmgb3 (15354)

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_008253.4, 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 TRCN0000071431 GAAGGATGTTGCTGACTATAA pLKO.1 741 CDS 100% 13.200 18.480 N Hmgb3 n/a
2 TRCN0000428612 GAAGGATGTTGCTGACTATAA pLKO_005 741 CDS 100% 13.200 18.480 N HMGB3 n/a
3 TRCN0000374016 GTAAGGTAGTGTTAACTATAT pLKO_005 1200 3UTR 100% 13.200 18.480 N Hmgb3 n/a
4 TRCN0000365844 AGGCAGATAAAGTCCGATATG pLKO_005 473 CDS 100% 10.800 15.120 N Hmgb3 n/a
5 TRCN0000071429 GCAGATAAAGTCCGATATGAT pLKO.1 475 CDS 100% 5.625 7.875 N Hmgb3 n/a
6 TRCN0000071430 CCGATATGATCGGGAGATGAA pLKO.1 486 CDS 100% 4.950 6.930 N Hmgb3 n/a
7 TRCN0000374095 GACATGCAGGGAAGAACATAA pLKO_005 342 CDS 100% 13.200 10.560 N Hmgb3 n/a
8 TRCN0000016705 GCTGGGTGAGATGTGGAATAA pLKO.1 657 CDS 100% 13.200 10.560 N HMGB3P1 n/a
9 TRCN0000365841 ACCCAGAGGTTCCCGTCAATT pLKO_005 371 CDS 100% 13.200 9.240 N Hmgb3 n/a
10 TRCN0000365843 GTGAGATGTGGAATAACTTAA pLKO_005 662 CDS 100% 13.200 9.240 N Hmgb3 n/a
11 TRCN0000365845 GTTGCTGACTATAAGTCTAAA pLKO_005 748 CDS 100% 13.200 9.240 N Hmgb3 n/a
12 TRCN0000365914 TATTGCCCTTGTTAGGTTTAA pLKO_005 957 3UTR 100% 13.200 9.240 N Hmgb3 n/a
13 TRCN0000374096 TCTAGCAAAGAGAAATCAAAG pLKO_005 436 CDS 100% 10.800 7.560 N Hmgb3 n/a
14 TRCN0000071428 GCGCCCTGAAACTGTATCAAA pLKO.1 1056 3UTR 100% 5.625 3.938 N Hmgb3 n/a
15 TRCN0000204085 GATGTCTGCTTATGCCTTCTT pLKO.1 315 CDS 100% 4.950 3.465 N HMGB3P27 n/a
16 TRCN0000071432 CCTGCTAAAGTTGCCCGGAAA pLKO.1 793 CDS 100% 4.050 2.835 N Hmgb3 n/a
17 TRCN0000018520 GCAAAGCTGAAGGAGAAGTAT pLKO.1 718 CDS 100% 5.625 3.375 N HMGB3 n/a
18 TRCN0000413041 AGGAAGAAGAGGAGGAGGAAG pLKO_005 845 CDS 100% 4.050 2.025 Y Myt1 n/a
19 TRCN0000163739 GAAGAAGAGGAAGAGGAGGAA pLKO.1 820 CDS 100% 2.640 1.320 Y CCDC88B 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_008253.4, 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_00752 pDONR223 100% 91.6% 97.5% None (many diffs) n/a
2 ccsbBroad304_00752 pLX_304 0% 91.6% 97.5% V5 (many diffs) n/a
3 ccsbBroadEn_10545 pDONR223 100% 57.5% 56% None (many diffs) n/a
4 ccsbBroad304_10545 pLX_304 0% 57.5% 56% V5 (many diffs) n/a
5 TRCN0000478096 GGTAGCAGCATCTGGTAAAACCTG pLX_317 52% 57.5% 56% V5 (many diffs) n/a
6 ccsbBroadEn_10544 pDONR223 100% 57.3% 56% None (many diffs) n/a
7 ccsbBroad304_10544 pLX_304 0% 57.3% 56% V5 (many diffs) n/a
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