Transcript: Human XM_011511065.3

PREDICTED: Homo sapiens homeobox D3 (HOXD3), transcript variant X2, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
HOXD3 (3232)
Length:
4374
CDS:
2248..3546

Additional Resources:

NCBI RefSeq record:
XM_011511065.3
NBCI Gene record:
HOXD3 (3232)

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 Human XM_011511065.3, 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 TRCN0000364174 TTTGGGTGACTCGCCATAAAT pLKO_005 3731 3UTR 100% 15.000 21.000 N HOXD3 n/a
2 TRCN0000378380 TAAGGATTGCATCGGACTAAA pLKO_005 3958 3UTR 100% 13.200 18.480 N HOXD3 n/a
3 TRCN0000019892 CGGCAACTTCGTCGAGTCCAT pLKO.1 3324 CDS 100% 0.880 1.232 N HOXD3 n/a
4 TRCN0000019889 CGCCAAATCACAGCCCAATAT pLKO.1 3153 CDS 100% 13.200 10.560 N HOXD3 n/a
5 TRCN0000378364 GCCAAATCACAGCCCAATATG pLKO_005 3154 CDS 100% 13.200 9.240 N HOXD3 n/a
6 TRCN0000364184 GAGCTTCCTGAGTGCACAATG pLKO_005 2278 CDS 100% 10.800 7.560 N HOXD3 n/a
7 TRCN0000019893 AGAAGGCTGCTTACTATGAAA pLKO.1 2300 CDS 100% 5.625 3.938 N HOXD3 n/a
8 TRCN0000019890 CCAGGACTGTTTGGAGGCTAT pLKO.1 2323 CDS 100% 4.050 2.835 N HOXD3 n/a
9 TRCN0000019891 TCGACAGAACTCCAAGCAGAA pLKO.1 2748 CDS 100% 4.050 2.835 N HOXD3 n/a
10 TRCN0000428137 GATCAAGATCTGGTTCCAGAA pLKO_005 2958 CDS 100% 4.050 2.025 Y Hoxa3 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_011511065.3, 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_06396 pDONR223 100% 99.9% 100% None 1051T>C n/a
2 ccsbBroad304_06396 pLX_304 0% 99.9% 100% V5 1051T>C n/a
3 TRCN0000492125 AATCTATAACATAAAAAGTGTCTC pLX_317 22.4% 99.9% 100% V5 1051T>C n/a
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