Transcript: Mouse XM_006527427.3

PREDICTED: Mus musculus pantothenate kinase 1 (Pank1), transcript variant X1, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Pank1 (75735)
Length:
4923
CDS:
518..1987

Additional Resources:

NCBI RefSeq record:
XM_006527427.3
NBCI Gene record:
Pank1 (75735)

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 BRDN0001147091 CCTATGTTGCTGGTTAACAT pXPR_003 GGG 1091 74% 3 0.277 Pank1 PANK1 76558
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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 XM_006527427.3, 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 TRCN0000024902 CCCGTGGTTTGGTATGGATAT pLKO.1 1075 CDS 100% 10.800 15.120 N Pank1 n/a
2 TRCN0000024901 GTACCCTATGTTGCTGGTTAA pLKO.1 1588 CDS 100% 0.000 0.000 N Pank1 n/a
3 TRCN0000361880 TACTGATCAGTGTGGTAATTT pLKO_005 2324 3UTR 100% 15.000 10.500 N Pank1 n/a
4 TRCN0000424569 AGTAATTACTCTAGGAGATTT pLKO_005 2356 3UTR 100% 13.200 9.240 N PANK1 n/a
5 TRCN0000368851 GCTCTTAGCTTTCAAGCTTAT pLKO_005 2123 3UTR 100% 10.800 7.560 N Pank1 n/a
6 TRCN0000368816 TCAATGAAGTTGCTAGCATAT pLKO_005 1853 CDS 100% 10.800 7.560 N Pank1 n/a
7 TRCN0000024900 GCAACATGATGAGCAAAGAAA pLKO.1 1683 CDS 100% 5.625 3.938 N Pank1 n/a
8 TRCN0000024903 CAGAATCAATATGGTCTCAAT pLKO.1 1837 CDS 100% 4.950 3.465 N Pank1 n/a
9 TRCN0000024899 CCGGAAGTATTTAACTTCTAA pLKO.1 1186 CDS 100% 0.563 0.394 N Pank1 n/a
10 TRCN0000194665 CCTATGTTGCTGGTTAACATG pLKO.1 1592 CDS 100% 0.495 0.347 N PANK1 n/a
11 TRCN0000361881 TTTGGAACATGAGGGTTATTT pLKO_005 1915 CDS 100% 15.000 9.000 N Pank1 n/a
12 TRCN0000428890 TGAAGAGCATCCGGAAGTATT pLKO_005 1176 CDS 100% 13.200 7.920 N PANK1 n/a
13 TRCN0000166364 CACACACACACACACACACAA pLKO.1 4212 3UTR 100% 4.950 2.475 Y KAAG1 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_006527427.3, 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_12021 pDONR223 100% 25.4% 21% None (many diffs) n/a
2 ccsbBroad304_12021 pLX_304 0% 25.4% 21% V5 (many diffs) n/a
3 TRCN0000475014 CCGGATTTTAACCCTTCACTGAGC pLX_317 100% 25.4% 21% V5 (many diffs) n/a
4 TRCN0000487959 CGACCGATTATTCACTTTGCAAAA pLX_317 72% 25.4% 21% V5 (not translated due to prior stop codon) (many diffs) n/a
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