Transcript: Human NM_001370340.1

Homo sapiens high mobility group box 1 (HMGB1), transcript variant 6, mRNA.

Source:
NCBI, updated 2019-09-10
Taxon:
Homo sapiens (human)
Gene:
HMGB1 (3146)
Length:
5687
CDS:
387..1034

Additional Resources:

NCBI RefSeq record:
NM_001370340.1
NBCI Gene record:
HMGB1 (3146)

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 Human NM_001370340.1, 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 Human Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000356492 GATGCAGCTTATACGAAATAA pLKO_005 1365 3UTR 100% 15.000 10.500 N HMGB1 n/a
2 TRCN0000347150 GTTGGTGCACAGCACAAATTA pLKO_005 1301 3UTR 100% 15.000 9.000 N Hmgb1-ps7 n/a
3 TRCN0000347067 AGAAGATGATGATGATGAATA pLKO_005 1013 CDS 100% 13.200 7.920 N Hmgb1-ps7 n/a
4 TRCN0000365913 GAAGATGATGATGATGAATAA pLKO_005 1014 CDS 100% 13.200 7.920 N Hmgb1 n/a
5 TRCN0000092693 GCACAGCACAAATTAGTTATA pLKO.1 1307 3UTR 100% 13.200 7.920 N Hmgb1-ps7 n/a
6 TRCN0000374090 TTGGTGCACAGCACAAATTAG pLKO_005 1302 3UTR 100% 13.200 7.920 N Hmgb1 n/a
7 TRCN0000018933 GCAGATGACAAGCAGCCTTAT pLKO.1 798 CDS 100% 10.800 6.480 N HMGB1 n/a
8 TRCN0000356565 TTGGTGATGTTGCGAAGAAAC pLKO_005 751 CDS 100% 10.800 6.480 N HMGB1 n/a
9 TRCN0000018932 CCGTTATGAAAGAGAAATGAA pLKO.1 593 CDS 100% 5.625 3.375 N HMGB1 n/a
10 TRCN0000018934 CCCAGATGCTTCAGTCAACTT pLKO.1 479 CDS 100% 4.950 2.970 N HMGB1 n/a
11 TRCN0000356490 ATTGCTGCATATCGAGCTAAA pLKO_005 861 CDS 100% 10.800 5.400 Y HMGB1 n/a
12 TRCN0000374091 GGAAGACCATGTCTGCTAAAG pLKO_005 532 CDS 100% 10.800 5.400 Y Hmgb1 n/a
13 TRCN0000222574 CGCCTGTAATCCCAGCACTTT pLKO.1 3782 3UTR 100% 4.950 2.475 Y ERAP2 n/a
14 TRCN0000018931 GAAGAAGATGAAGATGAAGAA pLKO.1 993 CDS 100% 4.950 2.475 Y HMGB1 n/a
15 TRCN0000092696 GAAGATGAAGAAGAAGATGAT pLKO.1 1002 CDS 100% 4.950 2.475 Y Hmgb1-ps7 n/a
16 TRCN0000093082 GAAGATGAAGATGAAGAAGAA pLKO.1 996 CDS 100% 4.950 2.475 Y Gm5518 n/a
17 TRCN0000093079 GATGAAGAAGAAGATGATGAT pLKO.1 1005 CDS 100% 4.950 2.475 Y Gm5518 n/a
18 TRCN0000138140 GATTGAGACCATCCTGGCTAA pLKO.1 3837 3UTR 100% 4.050 2.025 Y LOC441087 n/a
19 TRCN0000078113 GCCTGTAATCCCAGCACTTTA pLKO.1 3783 3UTR 100% 13.200 6.600 Y LIAS n/a
20 TRCN0000063714 GAAGAAGATGATGATGATGAT pLKO.1 1011 CDS 100% 4.950 2.475 Y SET n/a
21 TRCN0000288612 GAAGAAGATGATGATGATGAT pLKO_005 1011 CDS 100% 4.950 2.475 Y SET n/a
22 TRCN0000135549 GAGGAAGATGAAGAGGATGAA pLKO.1 957 CDS 100% 4.950 2.475 Y GRWD1 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_001370340.1, 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_06381 pDONR223 100% 99.6% 100% None 195A>G;465T>C n/a
2 ccsbBroad304_06381 pLX_304 0% 99.6% 100% V5 195A>G;465T>C n/a
3 TRCN0000471608 TGTAATATTACCATGCAATTGTTG pLX_317 34.2% 99.5% 100% V5 195A>G;465T>C;630A>G n/a
4 TRCN0000472460 CAGTTATAATCGGCCCACAAAGCC pLX_317 60.9% 98.7% 98.1% V5 (many diffs) n/a
5 ccsbBroadEn_14961 pDONR223 60% 96.1% 94.8% None (many diffs) n/a
6 ccsbBroad304_14961 pLX_304 0% 96.1% 94.8% V5 (many diffs) n/a
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