Transcript: Human NM_001128629.3

Homo sapiens BUB1B-PAK6 readthrough (BUB1B-PAK6), transcript variant 2, mRNA.

Source:
NCBI, updated 2019-06-02
Taxon:
Homo sapiens (human)
Gene:
BUB1B-PAK6 (106821730)
Length:
3796
CDS:
358..2403

Additional Resources:

NCBI RefSeq record:
NM_001128629.3
NBCI Gene record:
BUB1B-PAK6 (106821730)

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 BRDN0001145287 TCTGAGCGCACTGACCCCCA pXPR_003 CGG 419 20% 4 0.9698 BUB1B-PAK6, PAK6 PAK6 76923
2 BRDN0001146513 AGCTACGTGAAGATTGGCGA pXPR_003 GGG 1241 61% 5 0.3766 BUB1B-PAK6, PAK6 PAK6 76924
3 BRDN0001149511 GCACCCGTGTGATTCGCGAA pXPR_003 GGG 170 8% 3 0.1682 BUB1B-PAK6, PAK6 PAK6 76922
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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 Human NM_001128629.3, 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 Human Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000196369 GACCCTTTCTATCTAGATAAT pLKO.1 3611 3UTR 100% 13.200 6.600 Y PAK6 n/a
2 TRCN0000196314 GTGTTACCTTTCAAGTTTATC pLKO.1 3365 3UTR 100% 13.200 6.600 Y PAK6 n/a
3 TRCN0000001751 AGTGATCTCCAGGTCTTTGTA pLKO.1 2070 CDS 100% 5.625 2.813 Y PAK6 n/a
4 TRCN0000025187 CTGGACAGCTACGTGAAGATT pLKO.1 1576 CDS 100% 5.625 2.813 Y Pak6 n/a
5 TRCN0000001749 GCACAGGGATATTTCTAAGAA pLKO.1 2645 3UTR 100% 5.625 2.813 Y PAK6 n/a
6 TRCN0000001747 CATCCAGAAGTTGTCAGTCAT pLKO.1 621 CDS 100% 4.950 2.475 Y PAK6 n/a
7 TRCN0000195444 CCCAAAGAAGGCAAGTTTGTG pLKO.1 439 CDS 100% 4.950 2.475 Y PAK6 n/a
8 TRCN0000196965 GCACCAATAGGCATGGAATGA pLKO.1 989 CDS 100% 4.950 2.475 Y PAK6 n/a
9 TRCN0000197072 GCTCTCACTTTACAGAATGGA pLKO.1 3029 3UTR 100% 3.000 1.500 Y PAK6 n/a
10 TRCN0000001748 AGATCAGCAAAGACGTCCCTA pLKO.1 2006 CDS 100% 2.640 1.320 Y PAK6 n/a
11 TRCN0000195410 CCATGCTAAGTCTAACACTCC pLKO.1 3264 3UTR 100% 2.160 1.080 Y PAK6 n/a
12 TRCN0000199883 GCTCTCGGACTTCGGATTCTG pLKO.1 1980 CDS 100% 1.650 0.825 Y PAK6 n/a
13 TRCN0000001750 CGTCTCCCAAGTCAGGCTGAA pLKO.1 1833 CDS 100% 1.350 0.675 Y PAK6 n/a
14 TRCN0000199989 GCCACCGTACTTCAGTGACTC pLKO.1 2151 CDS 100% 1.350 0.675 Y PAK6 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_001128629.3, 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_03756 pDONR223 100% 100% 100% None n/a
2 ccsbBroad304_03756 pLX_304 0% 100% 100% V5 n/a
3 TRCN0000480942 ACTAGACGAACTCCGTGGCATTGG pLX_317 18.7% 100% 100% V5 n/a
4 ccsbBroadEn_15114 pDONR223 0% 100% 100% None n/a
5 ccsbBroad304_15114 pLX_304 0% 100% 100% V5 n/a
6 TRCN0000474094 CACGGGTCGCCTACTCATACCTGA pLX_317 22.2% 100% 100% V5 n/a
7 TRCN0000489778 TGGGGATCTGCTTCATCGTGAGCG pLX_317 17.4% 99.9% 100% V5 (not translated due to prior stop codon) 249G>A n/a
8 TRCN0000488099 AGATGGCCCCTTTGTAGTATGAAC pLX_317 16.6% 99.9% 99.8% V5 249G>A;2043_2044insG n/a
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