Transcript: Mouse XM_011245565.2

PREDICTED: Mus musculus family with sequence similarity 49, member B (Fam49b), transcript variant X6, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Fam49b (223601)
Length:
1772
CDS:
124..1098

Additional Resources:

NCBI RefSeq record:
XM_011245565.2
NBCI Gene record:
Fam49b (223601)

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_011245565.2, 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 TRCN0000215605 GAGTCGTATGAGAATTAATAA pLKO.1 612 CDS 100% 15.000 21.000 N Fam49b n/a
2 TRCN0000172577 GATGAGACTACCTCCAAGCAA pLKO.1 1057 CDS 100% 3.000 4.200 N FAM49B n/a
3 TRCN0000264757 ATTGAGTCGTATGAGAATTAA pLKO_005 609 CDS 100% 15.000 12.000 N Fam49b n/a
4 TRCN0000264756 TAATGGTGGGTGTCATAATAC pLKO_005 890 CDS 100% 13.200 10.560 N Fam49b n/a
5 TRCN0000193059 CCTTAAGTGATGCAACAACAA pLKO.1 722 CDS 100% 4.950 3.960 N Fam49b n/a
6 TRCN0000430901 ACTGCCTATTCTGCTATTTAA pLKO_005 1458 3UTR 100% 15.000 10.500 N FAM49B n/a
7 TRCN0000215668 GAGTCTGAGAAGGAAATATAT pLKO.1 211 CDS 100% 15.000 10.500 N Fam49b n/a
8 TRCN0000264755 GCCATCTAAGGCAGCTAATTA pLKO_005 1324 3UTR 100% 15.000 10.500 N Fam49b n/a
9 TRCN0000264754 CCGGAATACAGAAGCAGATTT pLKO_005 835 CDS 100% 13.200 9.240 N Fam49b n/a
10 TRCN0000264758 ATTGATATGAAAGGTTGTATC pLKO_005 958 CDS 100% 10.800 7.560 N Fam49b n/a
11 TRCN0000420983 ATTGATATGAAAGGTTGTATC pLKO_005 958 CDS 100% 10.800 7.560 N FAM49B n/a
12 TRCN0000172477 CCACGAAATACGAGAGGCAAT pLKO.1 303 CDS 100% 4.050 2.835 N FAM49B 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_011245565.2, 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_08323 pDONR223 100% 94.7% 99.3% None (many diffs) n/a
2 ccsbBroad304_08323 pLX_304 0% 94.7% 99.3% V5 (many diffs) n/a
3 TRCN0000472493 CGATGCATGTAAAACTTTATGGAA pLX_317 47% 94.7% 99.3% V5 (many diffs) n/a
4 ccsbBroadEn_03336 pDONR223 100% 94.7% 99.6% None (many diffs) n/a
5 ccsbBroad304_03336 pLX_304 0% 94.7% 99.6% V5 (many diffs) n/a
6 TRCN0000471959 TCGTCTAGCGGCAGCCCGTTTCCC pLX_317 38.5% 94.7% 99.6% V5 (many diffs) n/a
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