Transcript: Mouse NM_001313878.1

Mus musculus histone cluster 1 H2br (Hist1h2br), transcript variant 2, mRNA.

Source:
NCBI, updated 2017-01-31
Taxon:
Mus musculus (mouse)
Gene:
Hist1h2br (665622)
Length:
459
CDS:
29..409

Additional Resources:

NCBI RefSeq record:
NM_001313878.1
NBCI Gene record:
Hist1h2br (665622)

shRNA constructs matching this transcript with 100% SDR[?] match

This list includes all shRNAs that have a perfect SDR[?] match to Mouse NM_001313878.1, 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 Mouse Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000096962 CAAGGCCATGGGCATCATGAA pLKO.1 199 CDS 100% 4.950 2.475 Y Hist1h2bn n/a
2 TRCN0000435259 CAGAAGAAGGACGGCAAGAAG pLKO_005 95 CDS 100% 4.950 2.475 Y Hist1h2bg n/a
3 TRCN0000093062 CCAGAAGAAGGACGGCAAGAA pLKO.1 94 CDS 100% 4.950 2.475 Y Hist1h2bk n/a
4 TRCN0000438707 CCAGAAGAAGGACGGCAAGAA pLKO_005 94 CDS 100% 4.950 2.475 Y H2BC15 n/a
5 TRCN0000093095 CCAGAGTTCCAGTCTCATCAT pLKO.1 10 5UTR 100% 4.950 2.475 Y Hist1h2bq n/a
6 TRCN0000093117 CTACTCGGTGTACGTGTACAA pLKO.1 139 CDS 100% 4.950 2.475 Y Hist1h2bq n/a
7 TRCN0000442838 CTCCTAACCCAAAGGCTCTTT pLKO_005 426 3UTR 100% 4.950 2.475 Y Hist1h2bg n/a
8 TRCN0000282109 GCTACTCGGTGTACGTGTACA pLKO_005 138 CDS 100% 4.950 2.475 Y Hist1h2br n/a
9 TRCN0000446903 TACTCGGTGTACGTGTACAAG pLKO_005 140 CDS 100% 4.950 2.475 Y Hist1h2bg n/a
10 TRCN0000435792 ACAACAAGCGCTCGACCATCA pLKO_005 279 CDS 100% 4.050 2.025 Y Hist1h2bk n/a
11 TRCN0000445772 ACAACAAGCGCTCGACCATCA pLKO_005 279 CDS 100% 4.050 2.025 Y H2BC4 n/a
12 TRCN0000441789 ACGTGTACAAGGTGCTGAAGC pLKO_005 150 CDS 100% 4.050 2.025 Y H2BC13 n/a
13 TRCN0000262205 ATCATGAACTCGTTCGTGAAC pLKO_005 212 CDS 100% 4.050 2.025 Y Hist1h2br n/a
14 TRCN0000093137 CAAGGAGAGCTACTCGGTGTA pLKO.1 130 CDS 100% 4.050 2.025 Y Hist1h2bp n/a
15 TRCN0000093061 CATCATGAACTCGTTCGTGAA pLKO.1 211 CDS 100% 4.050 2.025 Y Hist1h2bk n/a
16 TRCN0000426446 CGTTCGTGAACGACATCTTCG pLKO_005 222 CDS 100% 4.050 2.025 Y Hist1h2bg n/a
17 TRCN0000433475 GAGCTACTCGGTGTACGTGTA pLKO_005 136 CDS 100% 4.050 2.025 Y Hist1h2bk n/a
18 TRCN0000093059 GTACGTGTACAAGGTGCTGAA pLKO.1 148 CDS 100% 4.050 2.025 Y Hist1h2bk n/a
19 TRCN0000262206 TACAACAAGCGCTCGACCATC pLKO_005 278 CDS 100% 4.050 2.025 Y Hist1h2br n/a
20 TRCN0000437414 TACAACAAGCGCTCGACCATC pLKO_005 278 CDS 100% 4.050 2.025 Y H2BC15 n/a
21 TRCN0000375583 TACGTGTACAAGGTGCTGAAG pLKO_005 149 CDS 100% 4.050 2.025 Y Hist1h2bb n/a
22 TRCN0000425656 TACGTGTACAAGGTGCTGAAG pLKO_005 149 CDS 100% 4.050 2.025 Y H2BC15 n/a
23 TRCN0000093135 GTGTACAAGGTGCTGAAGCAA pLKO.1 152 CDS 100% 3.000 1.500 Y Hist1h2bp n/a
24 TRCN0000096945 CACCAAGTACACCAGCTCCAA pLKO.1 385 CDS 100% 2.640 1.320 Y Hist1h2be n/a
25 TRCN0000093115 CATGGGCATCATGAACTCGTT pLKO.1 205 CDS 100% 2.640 1.320 Y Hist1h2bq n/a
26 TRCN0000096972 GCATCATGAACTCGTTCGTGA pLKO.1 210 CDS 100% 2.640 1.320 Y Hist1h2bl n/a
27 TRCN0000429678 GGGCATCATGAACTCGTTCGT pLKO_005 208 CDS 100% 2.640 1.320 Y Hist1h2bg n/a
28 TRCN0000096970 GTTCGTGAACGACATCTTCGA pLKO.1 223 CDS 100% 2.640 1.320 Y Hist1h2bl n/a
29 TRCN0000437950 TTACAACAAGCGCTCGACCAT pLKO_005 277 CDS 100% 2.640 1.320 Y Hist1h2bg n/a
30 TRCN0000093134 GAACGACATCTTCGAGCGCAT pLKO.1 229 CDS 100% 2.160 1.080 Y Hist1h2bp n/a
31 TRCN0000093060 CCCGAAGAAGGGCTCCAAGAA pLKO.1 58 CDS 100% 1.650 0.825 Y Hist1h2bk n/a
32 TRCN0000421762 CCGCCTGGCGCATTACAACAA pLKO_005 265 CDS 100% 1.650 0.825 Y Hist1h2bk n/a
33 TRCN0000093116 CGTCACCAAGGCCCAGAAGAA pLKO.1 82 CDS 100% 1.650 0.825 Y Hist1h2bq n/a
34 TRCN0000096961 CCCAGAAGAAGGACGGCAAGA pLKO.1 93 CDS 100% 1.350 0.675 Y Hist1h2bn n/a
35 TRCN0000093136 CTCCAAGAAGGCCGTCACCAA pLKO.1 70 CDS 100% 0.880 0.440 Y Hist1h2bp n/a
36 TRCN0000096973 GAAGGACGGCAAGAAGCGCAA pLKO.1 100 CDS 100% 0.720 0.360 Y Hist1h2bl n/a
37 TRCN0000093058 CTCGTTCGTGAACGACATCTT pLKO.1 220 CDS 100% 0.495 0.248 Y Hist1h2bk n/a
38 TRCN0000093147 GAACTCGTTCGTGAACGACAT pLKO.1 217 CDS 100% 0.405 0.203 Y Hist1h2bm n/a
39 TRCN0000096969 CGACACCGGCATCTCCTCCAA pLKO.1 181 CDS 100% 0.000 0.000 Y Hist1h2bl n/a
40 TRCN0000093133 CGGCATCTCCTCCAAGGCCAT pLKO.1 187 CDS 100% 0.000 0.000 Y Hist1h2bp n/a
41 TRCN0000096960 GAAGCGCAAGCGCAGCCGCAA pLKO.1 112 CDS 100% 0.000 0.000 Y Hist1h2bn n/a
42 TRCN0000096963 GCGCAGCCGCAAGGAGAGCTA pLKO.1 121 CDS 100% 0.000 0.000 Y Hist1h2bn n/a
43 TRCN0000096971 GCTCCAAGAAGGCCGTCACCA pLKO.1 69 CDS 100% 0.000 0.000 Y Hist1h2bl n/a
44 TRCN0000096977 ATGGGCATCATGAACTCGTTT pLKO.1 206 CDS 100% 4.950 2.475 Y Hist1h2bf n/a
45 TRCN0000096958 GACACCGGCATCTCCTCCAAA pLKO.1 182 CDS 100% 1.650 0.825 Y Hist1h2bh n/a
46 TRCN0000093066 TCGTTCGTGAACGACATCTTT pLKO.1 221 CDS 100% 0.563 0.281 Y Hist1h2bb 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_001313878.1, 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_01898 pDONR223 100% 93.6% 98.4% None (many diffs) n/a
2 ccsbBroad304_01898 pLX_304 0% 93.6% 98.4% V5 (many diffs) n/a
3 TRCN0000469156 CCCGCACAGGGATTAGCAAAGTTG pLX_317 89.9% 93.6% 98.4% V5 (many diffs) n/a
4 ccsbBroadEn_07224 pDONR223 100% 92.5% 98.4% None (many diffs) n/a
5 ccsbBroad304_07224 pLX_304 0% 92.5% 98.4% V5 (many diffs) n/a
6 TRCN0000472239 ATGAGCATATTTAAATGCTTTCTC pLX_317 100% 92.5% 98.4% V5 (many diffs) n/a
7 ccsbBroadEn_04472 pDONR223 100% 92.3% 98.4% None (many diffs) n/a
8 ccsbBroad304_04472 pLX_304 0% 92.3% 98.4% V5 (many diffs) n/a
9 TRCN0000471184 TCCCCACAGAAAAAGCTTCGCGAC pLX_317 82.9% 92.3% 98.4% V5 (many diffs) n/a
10 ccsbBroadEn_07223 pDONR223 100% 92% 98.4% None (many diffs) n/a
11 ccsbBroad304_07223 pLX_304 0% 92% 98.4% V5 (many diffs) n/a
12 TRCN0000471318 CGGCGACCCACTCTTCACCGCCCG pLX_317 96.2% 92% 98.4% V5 (many diffs) n/a
13 ccsbBroadEn_06348 pDONR223 100% 92% 99.2% None (many diffs) n/a
14 ccsbBroad304_06348 pLX_304 0% 92% 99.2% V5 (many diffs) n/a
15 TRCN0000466554 GCTTTTTGTCTTCCCTACTCACGT pLX_317 98.5% 92% 99.2% V5 (many diffs) n/a
16 ccsbBroadEn_01903 pDONR223 100% 92% 98.4% None (many diffs) n/a
17 ccsbBroad304_01903 pLX_304 0% 92% 98.4% V5 (many diffs) n/a
18 TRCN0000474598 ACTACAGCTCACCGGCGTAGGAAC pLX_317 100% 92% 98.4% V5 (many diffs) n/a
19 ccsbBroadEn_12031 pDONR223 100% 91.7% 96.8% None (many diffs) n/a
20 ccsbBroad304_12031 pLX_304 0% 91.7% 96.8% V5 (many diffs) n/a
21 TRCN0000469135 AACATACCTTGTTGTCATTTATTA pLX_317 100% 91.7% 96.8% V5 (many diffs) n/a
22 ccsbBroadEn_05671 pDONR223 100% 91.5% 97.6% None (many diffs) n/a
23 ccsbBroad304_05671 pLX_304 0% 91.5% 97.6% V5 (many diffs) n/a
24 TRCN0000476574 TAAAAAAACATGTTATCTATAAGA pLX_317 92.5% 91.5% 97.6% V5 (many diffs) n/a
25 ccsbBroadEn_15861 pDONR223 0% 91.5% 97.6% None (many diffs) n/a
26 ccsbBroad304_15861 pLX_304 0% 91.5% 97.6% V5 (many diffs) n/a
27 TRCN0000466058 TATAACTAACAAACAAGCTAACTT pLX_317 98.5% 91.5% 97.6% V5 (many diffs) n/a
28 ccsbBroadEn_01902 pDONR223 100% 91.5% 97.6% None (many diffs) n/a
29 ccsbBroad304_01902 pLX_304 0% 91.5% 97.6% V5 (many diffs) n/a
30 TRCN0000473896 CTGGCTTAAGACAGAATAAACCCC pLX_317 100% 91.5% 97.6% V5 (many diffs) n/a
31 ccsbBroadEn_01900 pDONR223 100% 91.2% 99.2% None (many diffs) n/a
32 ccsbBroad304_01900 pLX_304 0% 91.2% 99.2% V5 (many diffs) n/a
33 TRCN0000470158 AGTTTACTCTTCCCTTTATTAGAT pLX_317 90.5% 91.2% 99.2% V5 (many diffs) n/a
34 ccsbBroadEn_01901 pDONR223 100% 91% 98.4% None (many diffs) n/a
35 ccsbBroad304_01901 pLX_304 0% 91% 98.4% V5 (many diffs) n/a
36 TRCN0000468700 CGACGATGACTCTCCCTCATTTGA pLX_317 100% 91% 98.4% V5 (many diffs) n/a
37 ccsbBroadEn_04839 pDONR223 100% 89.6% 96% None (many diffs) n/a
38 ccsbBroad304_04839 pLX_304 0% 89.6% 96% V5 (many diffs) n/a
39 TRCN0000466986 TCACGGGATGAGCTCCAAAAATGA pLX_317 100% 89.6% 96% V5 (many diffs) n/a
40 ccsbBroadEn_01899 pDONR223 100% 88.3% 96% None (many diffs) n/a
41 ccsbBroad304_01899 pLX_304 0% 88.3% 96% V5 (many diffs) n/a
42 TRCN0000477535 GAGTATGATTCTCGACACACTATA pLX_317 98.5% 88.3% 96% V5 (many diffs) n/a
43 ccsbBroadEn_01897 pDONR223 100% 87.8% 99.2% None (many diffs) n/a
44 ccsbBroad304_01897 pLX_304 0% 87.8% 99.2% V5 (many diffs) n/a
45 TRCN0000471861 TGCACGGGACGCACCAAATGACCA pLX_317 90.4% 87.8% 99.2% V5 (many diffs) n/a
46 ccsbBroadEn_11267 pDONR223 100% 71% 74.6% None (many diffs) n/a
47 ccsbBroad304_11267 pLX_304 0% 71% 74.6% V5 (many diffs) n/a
48 TRCN0000469107 ATTTGGTTCAGATACTGGTGTTTT pLX_317 18.5% 71% 74.6% V5 (many diffs) n/a
49 ccsbBroadEn_11322 pDONR223 100% 55.2% 58.7% None (many diffs) n/a
50 ccsbBroad304_11322 pLX_304 0% 55.2% 58.7% V5 (many diffs) n/a
51 TRCN0000471205 GAGTACAAGAAACTGCTGAAATGG pLX_317 100% 55.2% 58.7% V5 (many diffs) n/a
52 ccsbBroadEn_10354 pDONR223 100% 48.6% 50.7% None (many diffs) n/a
53 ccsbBroad304_10354 pLX_304 0% 48.6% 50.7% V5 (many diffs) n/a
54 TRCN0000466355 TTCTAACCCCTTTGTAGACCAATG pLX_317 100% 48.6% 50.7% V5 (many diffs) n/a
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