Transcript: Mouse NM_010439.4

Mus musculus high mobility group box 1 (Hmgb1), transcript variant 2, mRNA.

Source:
NCBI, updated 2017-06-11
Taxon:
Mus musculus (mouse)
Gene:
Hmgb1 (15289)
Length:
2855
CDS:
173..820

Additional Resources:

NCBI RefSeq record:
NM_010439.4
NBCI Gene record:
Hmgb1 (15289)

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_010439.4, 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 TRCN0000071423 CCCTTTATGAATCAGATACAA pLKO.1 1982 3UTR 100% 5.625 7.875 N Hmgb1 n/a
2 TRCN0000365838 ATGCAGCTTATACGAAGATAA pLKO_005 1204 3UTR 100% 13.200 9.240 N Hmgb1 n/a
3 TRCN0000347150 GTTGGTGCACAGCACAAATTA pLKO_005 1086 3UTR 100% 15.000 7.500 Y Hmgb1-ps7 n/a
4 TRCN0000347067 AGAAGATGATGATGATGAATA pLKO_005 799 CDS 100% 13.200 6.600 Y Hmgb1-ps7 n/a
5 TRCN0000347066 AGAAGTATGAGAAGGATATTG pLKO_005 630 CDS 100% 13.200 6.600 Y Hmgb1-ps7 n/a
6 TRCN0000365913 GAAGATGATGATGATGAATAA pLKO_005 800 CDS 100% 13.200 6.600 Y Hmgb1 n/a
7 TRCN0000071427 GAGAAGTATGAGAAGGATATT pLKO.1 629 CDS 100% 13.200 6.600 Y Hmgb1 n/a
8 TRCN0000092693 GCACAGCACAAATTAGTTATA pLKO.1 1092 3UTR 100% 13.200 6.600 Y Hmgb1-ps7 n/a
9 TRCN0000374090 TTGGTGCACAGCACAAATTAG pLKO_005 1087 3UTR 100% 13.200 6.600 Y Hmgb1 n/a
10 TRCN0000347151 AGGCTGACAAGGCTCGTTATG pLKO_005 366 CDS 100% 10.800 5.400 Y Hmgb1-ps7 n/a
11 TRCN0000374091 GGAAGACCATGTCTGCTAAAG pLKO_005 318 CDS 100% 10.800 5.400 Y Hmgb1 n/a
12 TRCN0000365912 TGACAAGGCTCGTTATGAAAG pLKO_005 370 CDS 100% 10.800 5.400 Y Hmgb1 n/a
13 TRCN0000071424 GCCAAGCTGAAGGAGAAGTAT pLKO.1 617 CDS 100% 5.625 2.813 Y Hmgb1 n/a
14 TRCN0000093109 ACTAGGAGAGATGTGGAACAA pLKO.1 556 CDS 100% 4.950 2.475 Y LOC433185 n/a
15 TRCN0000092697 AGGCTCGTTATGAAAGAGAAA pLKO.1 375 CDS 100% 4.950 2.475 Y Hmgb1-ps7 n/a
16 TRCN0000093080 CCCGGATGCTTCTGTCAACTT pLKO.1 265 CDS 100% 4.950 2.475 Y Gm5518 n/a
17 TRCN0000374093 CGGATGCTTCTGTCAACTTCT pLKO_005 267 CDS 100% 4.950 2.475 Y Hmgb1 n/a
18 TRCN0000071426 CGGCCTTCTTCTTGTTCTGTT pLKO.1 471 CDS 100% 4.950 2.475 Y Hmgb1 n/a
19 TRCN0000092867 CTTCTCAGAGTTCTCCAAGAA pLKO.1 283 CDS 100% 4.950 2.475 Y LOC435219 n/a
20 TRCN0000092710 CTTCTTGTTCTGTTCTGAGTA pLKO.1 478 CDS 100% 4.950 2.475 Y LOC383761 n/a
21 TRCN0000092696 GAAGATGAAGAAGAAGATGAT pLKO.1 788 CDS 100% 4.950 2.475 Y Hmgb1-ps7 n/a
22 TRCN0000093079 GATGAAGAAGAAGATGATGAT pLKO.1 791 CDS 100% 4.950 2.475 Y Gm5518 n/a
23 TRCN0000374092 GATGACAAGCAGCCCTATGAG pLKO_005 587 CDS 100% 4.950 2.475 Y Hmgb1 n/a
24 TRCN0000093081 GATGAGGAAGAGGAGGAAGAA pLKO.1 758 CDS 100% 4.950 2.475 Y Gm5518 n/a
25 TRCN0000093112 TGCAAAGAAACTAGGAGAGAT pLKO.1 547 CDS 100% 4.950 2.475 Y LOC433185 n/a
26 TRCN0000071425 CCTGGCTTATCCATTGGTGAT pLKO.1 524 CDS 100% 4.050 2.025 Y Hmgb1 n/a
27 TRCN0000093110 CATATGCATTCTTTGTGCAAA pLKO.1 216 CDS 100% 0.000 0.000 Y LOC433185 n/a
28 TRCN0000093108 GCTCGTTATGAAAGAGAAATA pLKO.1 377 CDS 100% 13.200 6.600 Y LOC433185 n/a
29 TRCN0000063714 GAAGAAGATGATGATGATGAT pLKO.1 797 CDS 100% 4.950 2.475 Y SET n/a
30 TRCN0000288612 GAAGAAGATGATGATGATGAT pLKO_005 797 CDS 100% 4.950 2.475 Y SET n/a
31 TRCN0000153398 GAAGAGGAAGATGATGAGGAT pLKO.1 728 CDS 100% 2.640 1.320 Y NPM2 n/a
Download CSV

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_010439.4, 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.

Download CSV

All ORF constructs matching this transcript

Clone ID DNA Barcode Vector Sequenced %[?] Nuc. Match %[?] Prot. Match %[?] Epitope Tag Match Diffs[?] Addgene[?]
1 ccsbBroadEn_06381 pDONR223 100% 91.6% 99% None (many diffs) n/a
2 ccsbBroad304_06381 pLX_304 0% 91.6% 99% V5 (many diffs) n/a
3 TRCN0000471608 TGTAATATTACCATGCAATTGTTG pLX_317 34.2% 91.4% 99% V5 (many diffs) n/a
4 TRCN0000472460 CAGTTATAATCGGCCCACAAAGCC pLX_317 60.9% 90.8% 97.2% V5 (many diffs) n/a
5 ccsbBroadEn_14961 pDONR223 60% 89% 94.4% None (many diffs) n/a
6 ccsbBroad304_14961 pLX_304 0% 89% 94.4% V5 (many diffs) n/a
Download CSV