Transcript: Mouse NM_001282961.1

Mus musculus neurotrophic tyrosine kinase, receptor, type 2 (Ntrk2), transcript variant 3, mRNA.

Source:
NCBI, updated 2017-06-03
Taxon:
Mus musculus (mouse)
Gene:
Ntrk2 (18212)
Length:
8711
CDS:
629..3094

Additional Resources:

NCBI RefSeq record:
NM_001282961.1
NBCI Gene record:
Ntrk2 (18212)

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.

Clone ID Target Seq Vector PAM Seq Cut Position Cut % of CDS Length Exon On Target Score[?] Other Matching Genes Orig. Target Gene[?] Notes Addgene[?]
1 BRDN0001146295 TTGGTGATGCCAAAGTACTG pXPR_003 GGG 1542 63% 13 0.7383 Ntrk2 NTRK2 76469
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shRNA constructs matching this transcript with 100% SDR[?] match

This list includes all shRNAs that have a perfect SDR[?] match to Mouse NM_001282961.1, 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 TRCN0000023700 CCTTAAGGATAACGAACATTT pLKO.1 1374 CDS 100% 13.200 18.480 N Ntrk2 n/a
2 TRCN0000023699 CCGGCTTAAAGTTTGTGGCTT pLKO.1 930 CDS 100% 2.640 3.696 N Ntrk2 n/a
3 TRCN0000361390 CAGCAACCTGCGGCACATAAA pLKO_005 970 CDS 100% 13.200 9.240 N Ntrk2 n/a
4 TRCN0000023703 CATTCCAAGTTTGGCATGAAA pLKO.1 2000 CDS 100% 5.625 3.938 N Ntrk2 n/a
5 TRCN0000023701 CCACGGATGTTGCTGACCAAA pLKO.1 1881 CDS 100% 4.950 3.465 N Ntrk2 n/a
6 TRCN0000023416 GAGAGCATCATGTACAGGAAA pLKO.1 2792 CDS 100% 4.950 3.465 N LOC382761 n/a
7 TRCN0000023702 GCTTACAAAGCGTTTCTGAAA pLKO.1 947 CDS 100% 4.950 3.465 N Ntrk2 n/a
8 TRCN0000002246 CCTTGTTGTATTCCTGCCTTT pLKO.1 3515 3UTR 100% 4.050 2.835 N NTRK2 n/a
9 TRCN0000023415 GCTATCGAACAATGAGGTGAT pLKO.1 2893 CDS 100% 4.050 2.835 N LOC382761 n/a
10 TRCN0000361389 CCGGAGAACATCACGGAAATT pLKO_005 821 CDS 100% 13.200 7.920 N Ntrk2 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_001282961.1, 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_14721 pDONR223 0% 87.5% 93.9% None (many diffs) n/a
2 ccsbBroad304_14721 pLX_304 0% 87.5% 93.9% V5 (many diffs) n/a
3 TRCN0000480309 ACAATAAGTGTCCCAGTTAAGTTT pLX_317 14.3% 87.5% 93.9% V5 (many diffs) n/a
4 TRCN0000488063 CTCACTGTCGAGCAACCATACTGA pLX_317 13% 87.5% 93.9% V5 (many diffs) n/a
5 TRCN0000488161 TATCAGACTTTGGGGGGGCAAAAC pLX_317 12.7% 87.5% 93.9% V5 (not translated due to prior stop codon) (many diffs) n/a
6 ccsbBroadEn_01113 pDONR223 100% 49.8% 50.5% None (many diffs) n/a
7 ccsbBroad304_01113 pLX_304 0% 49.8% 50.5% V5 (many diffs) n/a
8 TRCN0000489350 CGCGGCAGTCTCCAGTCATTGATT pLX_317 37.3% 37.6% .8% V5 (not translated due to prior stop codon) (many diffs) n/a
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