Transcript: Human NM_031857.1

Homo sapiens protocadherin alpha 9 (PCDHA9), transcript variant 1, mRNA.

Source:
NCBI, updated 2019-08-03
Taxon:
Homo sapiens (human)
Gene:
PCDHA9 (9752)
Length:
5984
CDS:
725..3577

Additional Resources:

NCBI RefSeq record:
NM_031857.1
NBCI Gene record:
PCDHA9 (9752)

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 NM_031857.1, 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 TRCN0000427165 CATACGAGCTGCAGCCAGAAA pLKO_005 2547 CDS 100% 4.950 6.930 N PCDHA9 n/a
2 TRCN0000053276 CTGATTAGTGTGATCGACCTA pLKO.1 1835 CDS 100% 2.640 3.696 N PCDHA9 n/a
3 TRCN0000174236 CTGATTAGTGTGATCGACCTA pLKO.1 1835 CDS 100% 2.640 3.696 N PCDHA9 n/a
4 TRCN0000053273 CCTCTGCTTCCTCAGATTCAA pLKO.1 3090 CDS 100% 5.625 3.938 N PCDHA9 n/a
5 TRCN0000435675 GTCTAGCCTGTTGGTTCTCAC pLKO_005 2845 CDS 100% 4.050 2.835 N PCDHA9 n/a
6 TRCN0000436636 GCCTTTCTCCTTGTGCTGGAT pLKO_005 3048 CDS 100% 2.640 1.584 N PCDHA9 n/a
7 TRCN0000432568 CAGATGCCAACGGGCAGGTTA pLKO_005 1860 CDS 100% 1.650 0.990 N PCDHA9 n/a
8 TRCN0000053277 CGCGCCTGTTCCAGTTGGATT pLKO.1 906 CDS 100% 1.650 0.990 N PCDHA9 n/a
9 TRCN0000174237 CGCGCCTGTTCCAGTTGGATT pLKO.1 906 CDS 100% 1.650 0.990 N PCDHA9 n/a
10 TRCN0000056018 GCCTGAAACATCTGTATTATA pLKO.1 4621 3UTR 100% 15.000 7.500 Y PCDHA8 n/a
11 TRCN0000094754 GCTGCTACAGAAGTGCTTTAA pLKO.1 4593 3UTR 100% 13.200 6.600 Y Pcdha5 n/a
12 TRCN0000053274 CCAGTGATGTTTCTCCAGATA pLKO.1 1569 CDS 100% 4.950 2.475 Y PCDHA9 n/a
13 TRCN0000053275 CTGGAGGTAAATCTGCAGAAT pLKO.1 947 CDS 100% 4.950 2.475 Y PCDHA9 n/a
14 TRCN0000094877 ACAAATTCATTATCCCAGGAT pLKO.1 3381 CDS 100% 2.640 1.320 Y Pcdha8 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 NM_031857.1, 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_02234 pDONR223 100% 100% 100% None n/a
2 ccsbBroad304_02234 pLX_304 0% 100% 100% V5 n/a
3 TRCN0000476214 CTTCGGTCTAAGTTTTCTGTTTTA pLX_317 12.4% 100% 100% V5 n/a
4 ccsbBroadEn_10461 pDONR223 100% 80.7% 80.1% None (many diffs) n/a
5 ccsbBroad304_10461 pLX_304 0% 80.7% 80.1% V5 (not translated due to prior stop codon) (many diffs) n/a
6 TRCN0000491834 GGCGCATTCTGATCGATACCCATC pLX_317 13.2% 80.7% 80.1% V5 (not translated due to prior stop codon) (many diffs) n/a
7 ccsbBroadEn_03708 pDONR223 100% 70.6% 68.4% None (many diffs) n/a
8 ccsbBroad304_03708 pLX_304 0% 70.6% 68.4% V5 (many diffs) n/a
9 TRCN0000478347 GTTAGTGCAGTCTACCGATACGAT pLX_317 12.1% 70.6% 68.4% V5 (many diffs) n/a
10 ccsbBroadEn_03707 pDONR223 100% 59.5% 59.4% None (many diffs) n/a
11 ccsbBroad304_03707 pLX_304 0% 59.5% 59.4% V5 (many diffs) n/a
12 TRCN0000466780 TTAATTAGCTTAAAGCACGGCATA pLX_317 17.1% 59.5% 59.4% V5 (many diffs) n/a
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