Transcript: Mouse XM_006500631.3

PREDICTED: Mus musculus synovial sarcoma translocation gene on chromosome 18-like 1 (Ss18l1), transcript variant X1, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Ss18l1 (269397)
Length:
4501
CDS:
519..1658

Additional Resources:

NCBI RefSeq record:
XM_006500631.3
NBCI Gene record:
Ss18l1 (269397)

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 Mouse XM_006500631.3, 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 TRCN0000190201 CTATGTGTCTCGGACCAACAT pLKO.1 983 CDS 100% 4.950 6.930 N Ss18l1 n/a
2 TRCN0000229634 CTCGGACCAACATCAACATGC pLKO_005 991 CDS 100% 4.050 3.240 N SS18L1 n/a
3 TRCN0000192184 CAACATCAACATGCAGTCTAA pLKO.1 998 CDS 100% 4.950 3.465 N Ss18l1 n/a
4 TRCN0000217259 CATAGCAGACTCCAATCAGAA pLKO.1 638 CDS 100% 4.950 3.465 N Ss18l1 n/a
5 TRCN0000201573 CCAACATCAACATGCAGTCTA pLKO.1 997 CDS 100% 4.950 3.465 N Ss18l1 n/a
6 TRCN0000189835 GCCCATGAGTCAACAGTACTA pLKO.1 1262 CDS 100% 4.950 3.465 N Ss18l1 n/a
7 TRCN0000202387 GCCGTCTTACTCTAGGACATT pLKO.1 3265 3UTR 100% 4.950 3.465 N Ss18l1 n/a
8 TRCN0000189678 GCCTCCAACACAGAACATGAA pLKO.1 680 CDS 100% 4.950 3.465 N Ss18l1 n/a
9 TRCN0000189707 GTCAGCAGTATGGAAGCTACA pLKO.1 1555 CDS 100% 4.050 2.835 N Ss18l1 n/a
10 TRCN0000107154 CCACCACCTGATCCAGTGCAT pLKO.1 533 CDS 100% 0.880 0.616 N SS18L1 n/a
11 TRCN0000192748 GCTGTGTTAGTGTGTGTTAAT pLKO.1 3743 3UTR 100% 13.200 7.920 N Ss18l1 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_006500631.3, 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_15780 pDONR223 0% 81.7% 83.8% None (many diffs) n/a
2 ccsbBroad304_15780 pLX_304 0% 81.7% 83.8% V5 (many diffs) n/a
3 TRCN0000480057 AGTTACGAGTCCAATCGTATCTGG pLX_317 29.7% 81.7% 83.8% V5 (many diffs) n/a
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