Transcript: Mouse NM_010436.2

Mus musculus H2A histone family, member X (H2afx), mRNA.

Source:
NCBI, updated 2017-06-25
Taxon:
Mus musculus (mouse)
Gene:
H2afx (15270)
Length:
1414
CDS:
48..479

Additional Resources:

NCBI RefSeq record:
NM_010436.2
NBCI Gene record:
H2afx (15270)

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

This list includes all shRNAs that have a perfect SDR[?] match to Mouse NM_010436.2, 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 TRCN0000097006 GCGGAAAGGCCACTACGCCGA pLKO.1 152 CDS 100% 0.000 0.000 N H2afx n/a
2 TRCN0000348628 TGCTGGCCTCATACCAGTTGA pLKO_005 978 3UTR 100% 4.950 3.960 N H2afx n/a
3 TRCN0000348562 AGAAATGGATCACATTGTTTC pLKO_005 942 3UTR 100% 10.800 7.560 N H2afx n/a
4 TRCN0000097004 GCGACTCAACTACAACCCAAA pLKO.1 1184 3UTR 100% 4.050 2.835 N H2afx n/a
5 TRCN0000348629 GCGTCTTTGCTTCAGCTTGGT pLKO_005 865 3UTR 100% 2.640 1.848 N H2afx n/a
6 TRCN0000097005 CGAGTACCTCACTGCCGAGAT pLKO.1 215 CDS 100% 1.350 0.945 N H2afx n/a
7 TRCN0000335511 CGAGTACCTCACTGCCGAGAT pLKO_005 215 CDS 100% 1.350 0.945 N H2afx n/a
8 TRCN0000097007 GCTCGAGTACCTCACTGCCGA pLKO.1 212 CDS 100% 0.000 0.000 N H2afx n/a
9 TRCN0000074588 CAACAAGAAGACGCGCATCAT pLKO.1 266 CDS 100% 4.950 2.475 Y H2AC18 n/a
10 TRCN0000242129 CAACAAGAAGACGCGCATCAT pLKO_005 266 CDS 100% 4.950 2.475 Y Hist1h2ad n/a
11 TRCN0000242133 CAACGACGAGGAGCTCAACAA pLKO_005 314 CDS 100% 4.950 2.475 Y Hist1h2ag n/a
12 TRCN0000364413 CAACGACGAGGAGCTCAACAA pLKO_005 314 CDS 100% 4.950 2.475 Y H2AX n/a
13 TRCN0000097001 ACAACAAGAAGACGCGCATCA pLKO.1 265 CDS 100% 4.050 2.025 Y Hist2h2ac n/a
14 TRCN0000256521 ACAACAAGAAGACGCGCATCA pLKO_005 265 CDS 100% 4.050 2.025 Y H2AC19 n/a
15 TRCN0000257783 ACAAGAAGACGCGCATCATCC pLKO_005 268 CDS 100% 4.050 2.025 Y Hist1h2an n/a
16 TRCN0000429705 ACAAGAAGACGCGCATCATCC pLKO_005 268 CDS 100% 4.050 2.025 Y H2AC20 n/a
17 TRCN0000257997 GACAACAAGAAGACGCGCATC pLKO_005 264 CDS 100% 2.250 1.125 Y Hist1h2af n/a
18 TRCN0000092689 CGACAACAAGAAGACGCGCAT pLKO.1 263 CDS 100% 2.160 1.080 Y Hist2h2aa2 n/a
19 TRCN0000429526 CGACAACAAGAAGACGCGCAT pLKO_005 263 CDS 100% 2.160 1.080 Y H2AW n/a
20 TRCN0000369835 GCAACGACGAGGAGCTCAACA pLKO_005 313 CDS 100% 1.650 0.825 Y H2AC17 n/a
21 TRCN0000433810 CGACGAGGAGCTCAACAAGCT pLKO_005 317 CDS 100% 0.880 0.440 Y H2AW n/a
22 TRCN0000255257 CAAGAAGACGCGCATCATCCC pLKO_005 269 CDS 100% 0.720 0.360 Y Hist2h2ab n/a
23 TRCN0000097023 CGAGGAGCTCAACAAGCTGCT pLKO.1 320 CDS 100% 0.720 0.360 Y Hist1h2ae n/a
24 TRCN0000092692 GCGACAACAAGAAGACGCGCA pLKO.1 262 CDS 100% 0.180 0.090 Y Hist2h2aa2 n/a
25 TRCN0000242134 CAACATCCAGGCCGTGCTGCT pLKO_005 377 CDS 100% 0.000 0.000 Y Hist1h2ag n/a
26 TRCN0000097008 CCAAGGCCAAGTCGCGCTCTT pLKO.1 85 CDS 100% 0.000 0.000 Y H2afx n/a
27 TRCN0000335510 CCAAGGCCAAGTCGCGCTCTT pLKO_005 85 CDS 100% 0.000 0.000 Y H2afx n/a
28 TRCN0000255946 CCCGCGACAACAAGAAGACGC pLKO_005 259 CDS 100% 0.000 0.000 Y Hist1h2ah n/a
29 TRCN0000097030 CCGCAACGACGAGGAGCTCAA pLKO.1 311 CDS 100% 0.000 0.000 Y Hist1h2ab n/a
30 TRCN0000097032 CCTGCAGCTGGCCATCCGCAA pLKO.1 296 CDS 100% 0.000 0.000 Y Hist1h2ab n/a
31 TRCN0000073282 CCTGCCCAACATCCAGGCCGT pLKO.1 371 CDS 100% 0.000 0.000 Y H2AX n/a
32 TRCN0000242131 GCAGCTGGCCATCCGCAACGA pLKO_005 299 CDS 100% 0.000 0.000 Y Hist1h2ag n/a
33 TRCN0000097031 GCTGGCCATCCGCAACGACGA pLKO.1 302 CDS 100% 0.000 0.000 Y Hist1h2ab n/a
34 TRCN0000106913 ACTGCCGAGATCCTGGAGCTT pLKO.1 225 CDS 100% 0.880 0.528 N H2AW n/a
35 TRCN0000074592 GCCATCCGCAACGACGAGGAA pLKO.1 306 CDS 100% 0.000 0.000 Y H2AC18 n/a
36 TRCN0000106666 GCCGAGATCCTGGAGCTGGCT pLKO.1 228 CDS 100% 0.000 0.000 Y H2AC13 n/a
37 TRCN0000096998 GCTCAACAAGCTGCTGGGCAA pLKO.1 326 CDS 100% 0.720 0.360 Y Hist2h2aa1 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_010436.2, 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_00717 pDONR223 100% 92.5% 97.2% None (many diffs) n/a
2 ccsbBroad304_00717 pLX_304 0% 92.5% 97.2% V5 (many diffs) n/a
3 TRCN0000469289 TCCAAGCCCTCATTGGAGCTGGTC pLX_317 100% 92.5% 97.2% V5 (many diffs) n/a
4 ccsbBroadEn_04591 pDONR223 100% 80.2% 83.2% None (many diffs) n/a
5 ccsbBroad304_04591 pLX_304 0% 80.2% 83.2% V5 (many diffs) n/a
6 TRCN0000472223 CCTTGCTACGATGTATGAGACTTA pLX_317 100% 80.2% 83.2% V5 (many diffs) n/a
7 ccsbBroadEn_01891 pDONR223 100% 78.3% 83.2% None (many diffs) n/a
8 ccsbBroad304_01891 pLX_304 0% 78.3% 83.2% V5 (many diffs) n/a
9 TRCN0000481190 CGTGTTGGCCGTTCGATTTAGAAT pLX_317 98.5% 78.3% 83.2% V5 (many diffs) n/a
10 ccsbBroadEn_02055 pDONR223 100% 78.1% 83.2% None (many diffs) n/a
11 ccsbBroad304_02055 pLX_304 0% 78.1% 83.2% V5 (many diffs) n/a
12 TRCN0000466333 TGGGGTTTAATTGCATTCTTGTTA pLX_317 72.6% 78.1% 83.2% V5 (many diffs) n/a
13 ccsbBroadEn_01893 pDONR223 100% 77.9% 83.2% None (many diffs) n/a
14 ccsbBroad304_01893 pLX_304 97.8% 77.9% 83.2% V5 (many diffs) n/a
15 TRCN0000469277 CTTGTACACGCATGGACCTTCTTT pLX_317 100% 77.9% 83.2% V5 (many diffs) n/a
16 ccsbBroadEn_15630 pDONR223 0% 77.6% 83.2% None (many diffs) n/a
17 ccsbBroad304_15630 pLX_304 0% 77.6% 83.2% V5 (many diffs) n/a
18 TRCN0000466536 CGATTGTCATTCGGCCGACTATTC pLX_317 51.9% 77.6% 83.2% V5 (many diffs) n/a
19 ccsbBroadEn_01894 pDONR223 100% 77.6% 83.9% None (many diffs) n/a
20 ccsbBroad304_01894 pLX_304 0% 77.6% 83.9% V5 (many diffs) n/a
21 TRCN0000466135 ATCGATAACCATCGCTTACCTGGA pLX_317 72.6% 77.6% 83.9% V5 (many diffs) n/a
22 TRCN0000479809 GGTCGAATGGTCGCATTAGATTCC pLX_317 80.6% 77.4% 83.2% V5 (many diffs) n/a
23 ccsbBroadEn_15631 pDONR223 0% 77.2% 83.2% None (many diffs) n/a
24 ccsbBroad304_15631 pLX_304 0% 77.2% 83.2% V5 (many diffs) n/a
25 ccsbBroadEn_15629 pDONR223 0% 77.4% 83.9% None (many diffs) n/a
26 ccsbBroad304_15629 pLX_304 0% 77.4% 83.9% V5 (many diffs) n/a
27 TRCN0000469353 AGACAGTAAACCCGGGATGCGCAC pLX_317 73.4% 77.4% 83.9% V5 (many diffs) n/a
28 ccsbBroadEn_01892 pDONR223 100% 77.2% 83.2% None (many diffs) n/a
29 ccsbBroad304_01892 pLX_304 0% 77.2% 83.2% V5 (many diffs) n/a
30 TRCN0000473552 GACAAACTTCCATCCTCTTGAACC pLX_317 98.5% 77.2% 83.2% V5 (many diffs) n/a
31 ccsbBroadEn_11266 pDONR223 100% 77.2% 83.2% None (many diffs) n/a
32 ccsbBroad304_11266 pLX_304 0% 77.2% 83.2% V5 (many diffs) n/a
33 TRCN0000473665 CTTGAACTGGACTCCCACCGCACC pLX_317 98.5% 77.2% 83.2% V5 (many diffs) n/a
34 ccsbBroadEn_01895 pDONR223 100% 76.7% 83.2% None (many diffs) n/a
35 ccsbBroad304_01895 pLX_304 0% 76.7% 83.2% V5 (many diffs) n/a
36 TRCN0000468567 AACCATAGCTAACCCTGCACACAC pLX_317 100% 76.7% 83.2% V5 (many diffs) n/a
37 ccsbBroadEn_15628 pDONR223 0% 76.3% 81.8% None (many diffs) n/a
38 ccsbBroad304_15628 pLX_304 0% 76.3% 81.8% V5 (many diffs) n/a
39 TRCN0000474646 TCTACAGTCTCGTAGCTATGTTCA pLX_317 100% 76.3% 81.8% V5 (many diffs) n/a
40 ccsbBroadEn_07222 pDONR223 100% 76.1% 81.8% None (many diffs) n/a
41 ccsbBroad304_07222 pLX_304 0% 76.1% 81.8% V5 (many diffs) n/a
42 TRCN0000474296 CCGAGAACTTAGACACGTTCATCC pLX_317 98.5% 76.1% 81.8% V5 (many diffs) n/a
43 ccsbBroadEn_03650 pDONR223 100% 76.1% 81.9% None (many diffs) n/a
44 ccsbBroad304_03650 pLX_304 0% 76.1% 81.9% V5 (many diffs) n/a
45 TRCN0000478286 ACAGCCCAAGTATGTTGCTGTGAT pLX_317 83.7% 76.1% 81.9% V5 (many diffs) n/a
46 ccsbBroadEn_01896 pDONR223 100% 75.9% 83.2% None (many diffs) n/a
47 ccsbBroad304_01896 pLX_304 0% 75.9% 83.2% V5 (many diffs) n/a
48 TRCN0000480994 TCCGAGTATGCGTATGATAAGCCC pLX_317 94.3% 75.9% 83.2% V5 (many diffs) n/a
49 ccsbBroadEn_09253 pDONR223 100% 74.9% 81.8% None (many diffs) n/a
50 ccsbBroad304_09253 pLX_304 0% 74.9% 81.8% V5 (many diffs) n/a
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