Transcript: Human XM_011524050.1

PREDICTED: Homo sapiens ubiquitin specific peptidase 6 (USP6), transcript variant X1, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
USP6 (9098)
Length:
8723
CDS:
2449..6669

Additional Resources:

NCBI RefSeq record:
XM_011524050.1
NBCI Gene record:
USP6 (9098)

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 Human XM_011524050.1, 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 Human Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000007337 GCGGAAGGACATACTTATGAA pLKO.1 2490 CDS 100% 5.625 7.875 N USP6 n/a
2 TRCN0000230365 GGAGCGGAAGGACATACTTAT pLKO_005 2487 CDS 100% 13.200 9.240 N USP6 n/a
3 TRCN0000230367 TCATGCCCAGGATCGTGATAA pLKO_005 5262 CDS 100% 13.200 9.240 N USP6 n/a
4 TRCN0000011088 TGCGGAACCAATTCTTCGATA pLKO.1 3416 CDS 100% 4.950 3.465 N USP6 n/a
5 TRCN0000007336 CGTTGGAATCAACAGCAGCAT pLKO.1 2562 CDS 100% 2.640 1.848 N USP6 n/a
6 TRCN0000218643 GCTTCTAGTCCAACACAAATA pLKO_005 4858 CDS 100% 13.200 7.920 N USP6 n/a
7 TRCN0000230368 ACCTGGACATGTCCCATTAAA pLKO_005 8305 3UTR 100% 15.000 7.500 Y USP6 n/a
8 TRCN0000230366 GGGAGAATGGGAGACATATAA pLKO_005 2691 CDS 100% 15.000 7.500 Y USP6 n/a
9 TRCN0000011161 CCAAAGAGAAGACACTCATAT pLKO.1 6351 CDS 100% 13.200 6.600 Y USP32P2 n/a
10 TRCN0000011157 CCCAGACATTAGGAGTTCATA pLKO.1 7704 3UTR 100% 5.625 2.813 Y USP32P2 n/a
11 TRCN0000011159 GCACAATTTCTGCCAAAGATT pLKO.1 6568 CDS 100% 5.625 2.813 Y USP32P2 n/a
12 TRCN0000007335 CCCTGCAAGTTGATTCTCATT pLKO.1 8010 3UTR 100% 4.950 2.475 Y USP6 n/a
13 TRCN0000011160 CCTTCCTGATTATTCACCTTA pLKO.1 5669 CDS 100% 4.950 2.475 Y USP32P2 n/a
14 TRCN0000011087 CCTCCTGAACATTCAGGAAAT pLKO.1 2784 CDS 100% 1.080 0.540 Y USP6 n/a
15 TRCN0000262629 GGTCAGTCCTCCTGAACATTG pLKO_005 2777 CDS 100% 10.800 5.400 Y TBC1D3H n/a
16 TRCN0000118541 CAAGCATCTTAGGGCCTCTAT pLKO.1 3465 CDS 100% 4.950 2.475 Y TBC1D3B 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_011524050.1, 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 TRCN0000492225 TATACGCCTCCTCACCATAAATTC pLX_317 8% 69.1% 58.4% V5 (not translated due to prior stop codon) (many diffs) n/a
2 TRCN0000488115 GTCATCACGCGGCCGTTATCCCAT pLX_317 7.3% 69.1% 58.3% V5 (many diffs) n/a
3 ccsbBroadEn_10145 pDONR223 100% 33.9% 29.9% None (many diffs) n/a
4 ccsbBroad304_10145 pLX_304 0% 33.9% 29.9% V5 (many diffs) n/a
5 ccsbBroadEn_13692 pDONR223 100% 21.4% 18.6% None (many diffs) n/a
6 ccsbBroad304_13692 pLX_304 0% 21.4% 18.6% V5 (many diffs) n/a
7 TRCN0000471618 GCCCATAACCCTACGTGGCCAATT pLX_317 40.7% 21.4% 18.6% V5 (many diffs) n/a
8 ccsbBroadEn_12794 pDONR223 100% 18% 14.6% None (many diffs) n/a
9 ccsbBroad304_12794 pLX_304 0% 18% 14.6% V5 (many diffs) n/a
10 ccsbBroadEn_11333 pDONR223 100% 11.1% 11% None 1_6delATGGAC;155_156ins183;496_4218del n/a
11 ccsbBroad304_11333 pLX_304 0% 11.1% 11% V5 1_6delATGGAC;155_156ins183;496_4218del n/a
12 TRCN0000471012 TAGTACGAGTCAGATGCACTGGCC pLX_317 54.4% 11.1% 11% V5 1_6delATGGAC;155_156ins183;496_4218del n/a
13 ccsbBroadEn_13327 pDONR223 100% 4.9% 4.3% None (many diffs) n/a
14 ccsbBroad304_13327 pLX_304 0% 4.9% 4.3% V5 (many diffs) n/a
15 TRCN0000476448 GTATAATACAGCTCGGATCTAGCC pLX_317 100% 4.9% 4.3% V5 (many diffs) n/a
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