Transcript: Human XM_006718843.4

PREDICTED: Homo sapiens ATM serine/threonine kinase (ATM), transcript variant X2, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
ATM (472)
Length:
9892
CDS:
153..9323

Additional Resources:

NCBI RefSeq record:
XM_006718843.4
NBCI Gene record:
ATM (472)

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 BRDN0001149033 GACCTACCTGAATAACACAC pXPR_003 TGG 5161 56% 34 1.0665 ATM ATM 77531
2 BRDN0001146099 TCTACCCCAACAGCGACATG pXPR_003 GGG 1342 15% 10 0.7458 ATM ATM 77530
3 BRDN0001149518 TCATCACCAAGTTCGCATGT pXPR_003 TGG 3259 36% 22 0.2508 ATM ATM 77529
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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_006718843.4, 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 TRCN0000196661 GCCATATTCTTTCCGTCTATT pLKO.1 6373 CDS 100% 13.200 18.480 N ATM n/a
2 TRCN0000038657 GCACTGAAAGAGGATCGTAAA pLKO.1 7512 CDS 100% 10.800 15.120 N ATM n/a
3 TRCN0000038658 CGTGTCTTAATGAGACTACAA pLKO.1 9174 CDS 100% 4.950 6.930 N ATM n/a
4 TRCN0000039952 GCTAGAATAATTCATGCTGTT pLKO.1 714 CDS 100% 4.050 5.670 N ATM n/a
5 TRCN0000195732 CTGGTGACTATACAGTCATTT pLKO.1 8190 CDS 100% 1.320 1.848 N ATM n/a
6 TRCN0000039949 GCACGCTAGAACCTACCAAAT pLKO.1 2953 CDS 100% 10.800 8.640 N ATM n/a
7 TRCN0000038654 CCTGCCAACATACTTTAAGTA pLKO.1 9389 3UTR 100% 5.625 4.500 N ATM n/a
8 TRCN0000038655 GCCGTCAACTAGAACATGATA pLKO.1 187 CDS 100% 5.625 4.500 N ATM n/a
9 TRCN0000245106 GCCGTCAACTAGAACATGATA pLKO_005 187 CDS 100% 5.625 4.500 N ATM n/a
10 TRCN0000245107 CGAGATCCTGAAACAATTAAA pLKO_005 255 CDS 100% 15.000 10.500 N ATM n/a
11 TRCN0000194969 CAAACGAAATCTCAGTGATAT pLKO.1 9125 CDS 100% 13.200 9.240 N ATM n/a
12 TRCN0000039950 CCTGAAACTTTGGATGAAATT pLKO.1 3573 CDS 100% 13.200 9.240 N ATM n/a
13 TRCN0000038656 GCCATAATTCAGGGTAGTTTA pLKO.1 1680 CDS 100% 13.200 9.240 N ATM n/a
14 TRCN0000245109 TGGGTGTGATCTTCAGTATAT pLKO_005 9315 CDS 100% 13.200 9.240 N ATM n/a
15 TRCN0000245108 TGGTCAAATACTTCATCAAAT pLKO_005 451 CDS 100% 13.200 9.240 N ATM n/a
16 TRCN0000194686 CCTGCGATTGTTAACATCAAA pLKO.1 2561 CDS 100% 5.625 3.938 N ATM n/a
17 TRCN0000039948 CCTTTCATTCAGCCTTTAGAA pLKO.1 9343 3UTR 100% 5.625 3.938 N ATM n/a
18 TRCN0000194861 CCAAGGTCTATGATATGCTTA pLKO.1 4099 CDS 100% 4.950 3.465 N ATM n/a
19 TRCN0000039951 GCCTCCAATTCTTCACAGTAA pLKO.1 1937 CDS 100% 4.950 3.465 N ATM n/a
20 TRCN0000010299 TGATGGTCTTAAGGAACATCT pLKO.1 9493 3UTR 100% 4.950 3.465 N ATM n/a
21 TRCN0000196335 GTATTACCTTTCGTGGTATAA pLKO.1 1618 CDS 100% 13.200 7.920 N ATM n/a
22 TRCN0000222574 CGCCTGTAATCCCAGCACTTT pLKO.1 9566 3UTR 100% 4.950 2.475 Y ERAP2 n/a
23 TRCN0000078113 GCCTGTAATCCCAGCACTTTA pLKO.1 9567 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_006718843.4, 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 ccsbBroadEn_10689 pDONR223 100% 4.2% 4.2% None 1_4044del;4438_9168del n/a
2 ccsbBroad304_10689 pLX_304 97.8% 4.2% 4.2% V5 1_4044del;4438_9168del n/a
3 TRCN0000471841 AACTATAAGACCCGGATATGCACT pLX_317 100% 4.2% 4.2% V5 1_4044del;4438_9168del n/a
4 ccsbBroadEn_10688 pDONR223 100% 3.6% 3.5% None 332_333insTA;335_9168del n/a
5 ccsbBroad304_10688 pLX_304 97.4% 3.6% 3.5% V5 332_333insTA;335_9168del n/a
6 TRCN0000491887 TGGTATTGATTCTCGAAGGTGCCG pLX_317 91.8% 3.6% 3.5% V5 332_333insTA;335_9168del n/a
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