Transcript: Human XM_005255184.4

PREDICTED: Homo sapiens SMG1 nonsense mediated mRNA decay associated PI3K related kinase (SMG1), transcript variant X5, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
SMG1 (23049)
Length:
16002
CDS:
378..11291

Additional Resources:

NCBI RefSeq record:
XM_005255184.4
NBCI Gene record:
SMG1 (23049)

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 BRDN0001149508 CGTGTTCAACTAGTGCACAG pXPR_003 TGG 2267 21% 17 0.2782 SMG1 SMG1 75772
2 BRDN0001146980 TAGTGTCGAGCATGGAACCG pXPR_003 GGG 6405 59% 40 0.1095 SMG1 SMG1 75770
3 BRDN0001149395 GTAGATTCACTCTCGATCCG pXPR_003 AGG 4593 42% 30 0.0619 SMG1 SMG1 75771
4 BRDN0001144779 GAACGCTTCAGCCCAATTCG pXPR_003 GGG 1100 10% 9 0.054 SMG1 SMG1 75769
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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 XM_005255184.4, 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 TRCN0000244937 CAGTATCCGAAGGCCATATTT pLKO_005 8253 CDS 100% 15.000 21.000 N SMG1 n/a
2 TRCN0000196275 GCTTAGCTTGTGTAGTTATTT pLKO.1 14280 3UTR 100% 15.000 21.000 N SMG1 n/a
3 TRCN0000037410 GCCATGACTAACACTGAAATT pLKO.1 6522 CDS 100% 13.200 18.480 N SMG1 n/a
4 TRCN0000194827 CGTTAATCTGTAATCGTTAAG pLKO.1 13251 3UTR 100% 10.800 15.120 N SMG1 n/a
5 TRCN0000037409 GCCGAGATGTTGATCCGAATA pLKO.1 11170 CDS 100% 10.800 15.120 N SMG1 n/a
6 TRCN0000197107 GCGTTGTCAAGAGCTCTATAG pLKO.1 8339 CDS 100% 10.800 15.120 N SMG1 n/a
7 TRCN0000196627 GCTGTAGTTATGAAGTCATAC pLKO.1 14016 3UTR 100% 10.800 15.120 N SMG1 n/a
8 TRCN0000244939 ATGCCTCCTGATGGATATAAT pLKO_005 15811 3UTR 100% 15.000 12.000 N SMG1 n/a
9 TRCN0000244938 GAGTTAGAGCTTCGTTTATTA pLKO_005 10350 CDS 100% 15.000 12.000 N SMG1 n/a
10 TRCN0000195729 CGGCGTTATTTGAACTAATCA pLKO.1 10276 CDS 100% 5.625 4.500 N SMG1 n/a
11 TRCN0000196849 GCTTTACTATTCGCACATTTA pLKO.1 14985 3UTR 100% 13.200 9.240 N SMG1 n/a
12 TRCN0000196274 GCATTCAGATTCTCGTGTAAC pLKO.1 11746 3UTR 100% 10.800 7.560 N SMG1 n/a
13 TRCN0000037411 CCCAATTAGAAGCCATCTCAT pLKO.1 4466 CDS 100% 4.950 3.465 N SMG1 n/a
14 TRCN0000037412 CGGCAAATCATATTTCCAGAA pLKO.1 8889 CDS 100% 4.050 2.835 N SMG1 n/a
15 TRCN0000194789 CCAACTTTACTTGGCAATATT pLKO.1 5868 CDS 100% 15.000 9.000 N SMG1 n/a
16 TRCN0000244936 GTGCAACTGAAGGAGTTATTA pLKO_005 5392 CDS 100% 15.000 9.000 N SMG1 n/a
17 TRCN0000037413 GCACTGTAACTACGGCTACAA pLKO.1 2311 CDS 100% 4.950 2.970 N SMG1 n/a
18 TRCN0000244935 CTCGATGTTACCCTCATATTT pLKO_005 1132 CDS 100% 15.000 7.500 Y SMG1 n/a
19 TRCN0000222574 CGCCTGTAATCCCAGCACTTT pLKO.1 12819 3UTR 100% 4.950 2.475 Y ERAP2 n/a
20 TRCN0000183297 GCTTGAAGAATATTCCTGTTT pLKO.1 1882 CDS 100% 4.950 2.475 Y BOLA2 n/a
21 TRCN0000078113 GCCTGTAATCCCAGCACTTTA pLKO.1 12820 3UTR 100% 13.200 6.600 Y LIAS 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_005255184.4, 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 TRCN0000488255 ACGTTGGAAAGGGAAAGCTGGCTT pLX_317 1.7% 97.7% 97.8% V5 (not translated due to prior stop codon) (many diffs) n/a
2 ccsbBroadEn_10398 pDONR223 100% 2.8% 2.7% None (many diffs) n/a
3 ccsbBroad304_10398 pLX_304 0% 2.8% 2.7% V5 (many diffs) n/a
4 TRCN0000474199 GATTATACATTTATGTAATCCGTA pLX_317 93.9% 2.8% 2.7% V5 (many diffs) n/a
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