Transcript: Mouse XM_006505359.3

PREDICTED: Mus musculus Braf transforming gene (Braf), transcript variant X10, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Braf (109880)
Length:
13591
CDS:
125..2710

Additional Resources:

NCBI RefSeq record:
XM_006505359.3
NBCI Gene record:
Braf (109880)

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 XM_006505359.3, 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 TRCN0000022593 CCAGCTACCTTATTCAAACAT pLKO.1 2365 CDS 100% 5.625 7.875 N Braf n/a
2 TRCN0000307373 CCAGCTACCTTATTCAAACAT pLKO_005 2365 CDS 100% 5.625 7.875 N Braf n/a
3 TRCN0000054347 CCGTTGTCAAACATGTGGTTA pLKO.1 1183 CDS 100% 4.950 6.930 N Braf n/a
4 TRCN0000287177 CCGTTGTCAAACATGTGGTTA pLKO_005 1183 CDS 100% 4.950 6.930 N Braf n/a
5 TRCN0000054345 CCACATCATTGAGACCAAATT pLKO.1 2032 CDS 100% 13.200 9.240 N Braf n/a
6 TRCN0000287179 CCACATCATTGAGACCAAATT pLKO_005 2032 CDS 100% 13.200 9.240 N Braf n/a
7 TRCN0000195609 CTCAGTAAGGTACGGAGTAAC pLKO.1 2441 CDS 100% 10.800 7.560 N BRAF n/a
8 TRCN0000196918 GAACATATAGAGGCCCTATTG pLKO.1 581 CDS 100% 10.800 7.560 N BRAF n/a
9 TRCN0000022592 CACCACAGAAACCTATCGTTA pLKO.1 858 CDS 100% 4.950 3.465 N Braf n/a
10 TRCN0000294553 CACCACAGAAACCTATCGTTA pLKO_005 858 CDS 100% 4.950 3.465 N Braf n/a
11 TRCN0000022590 CCCACTTACAACACACAACTT pLKO.1 1096 CDS 100% 4.950 3.465 N Braf n/a
12 TRCN0000054343 GCTACCTTATTCAAACATCAA pLKO.1 2368 CDS 100% 4.950 3.465 N Braf n/a
13 TRCN0000054346 CGAGGATACCTATCTCCAGAT pLKO.1 2420 CDS 100% 4.050 2.835 N Braf n/a
14 TRCN0000287119 CGAGGATACCTATCTCCAGAT pLKO_005 2420 CDS 100% 4.050 2.835 N Braf n/a
15 TRCN0000054344 GCAGATGAAGATCATCGCAAT pLKO.1 1448 CDS 100% 4.050 2.835 N Braf n/a
16 TRCN0000302346 GCAGATGAAGATCATCGCAAT pLKO_005 1448 CDS 100% 4.050 2.835 N Braf n/a
17 TRCN0000022589 CCTGGGTAATGGAGCAGATTT pLKO.1 712 CDS 100% 13.200 7.920 N Braf 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 XM_006505359.3, 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_00174 pDONR223 100% 82.4% 86.6% None (many diffs) n/a
2 ccsbBroad304_00174 pLX_304 0% 82.4% 86.6% V5 (many diffs) n/a
3 TRCN0000478042 TCTGAATTAGGGTTGATCCCCCGC pLX_317 17.9% 82.4% 86.6% V5 (many diffs) n/a
4 TRCN0000489575 CGTTCGGAATTCTGTGTTGTACCC pLX_317 15.7% 82.4% 86.6% V5 (not translated due to prior stop codon) (many diffs) n/a
5 TRCN0000489494 GTTAACTACCATGGAAACCTGCTA pLX_317 14.9% 82.4% 86.6% V5 (not translated due to prior stop codon) (many diffs) n/a
6 ccsbBroadEn_16175 pDONR223 0% 82.4% 86.5% None (many diffs) n/a
7 ccsbBroad304_16175 pLX_304 0% 82.4% 86.5% V5 (many diffs) n/a
8 TRCN0000491583 CCCTCTGATACCGCCGCCACCAGA pLX_317 17.6% 82.4% 86.5% V5 (not translated due to prior stop codon) (many diffs) n/a
9 ccsbBroadEn_14553 pDONR223 65.1% 77% 22.4% None (many diffs) n/a
10 ccsbBroad304_14553 pLX_304 0% 77% 22.4% V5 (not translated due to prior stop codon) (many diffs) n/a
11 TRCN0000480310 GCCCGGTAACTCGCTTTGGCCAAA pLX_317 17.4% 77% 22.4% V5 (not translated due to prior stop codon) (many diffs) n/a
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