Transcript: Human NM_003574.6

Homo sapiens VAMP associated protein A (VAPA), transcript variant 1, mRNA.

Source:
NCBI, updated 2019-09-29
Taxon:
Homo sapiens (human)
Gene:
VAPA (9218)
Length:
6936
CDS:
242..1126

Additional Resources:

NCBI RefSeq record:
NM_003574.6
NBCI Gene record:
VAPA (9218)

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_003574.6, 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 TRCN0000293263 TCCAAATTGAGATGCGTATTT pLKO_005 611 CDS 100% 13.200 18.480 N VAPA n/a
2 TRCN0000298476 GCTCCGACTGTCACTTCAATG pLKO_005 680 CDS 100% 10.800 15.120 N VAPA n/a
3 TRCN0000382188 AGTTTATGGTACAGACAATTT pLKO_005 522 CDS 100% 13.200 9.240 N VAPA n/a
4 TRCN0000293204 ATCCGCCCACAGACCTCAAAT pLKO_005 294 CDS 100% 13.200 9.240 N VAPA n/a
5 TRCN0000093609 GCTAATATCATGGCAGAATTT pLKO.1 1611 3UTR 100% 13.200 9.240 N Vapa n/a
6 TRCN0000380637 GCTAATATCATGGCAGAATTT pLKO_005 1611 3UTR 100% 13.200 9.240 N VAPA n/a
7 TRCN0000382387 TTGCAACACCTGCCAGTTATC pLKO_005 720 CDS 100% 10.800 7.560 N VAPA n/a
8 TRCN0000029133 CACTTAATGATACCGAAACAA pLKO.1 873 CDS 100% 5.625 3.938 N VAPA n/a
9 TRCN0000029129 GCCAGTTATCACACGAAGGAT pLKO.1 731 CDS 100% 3.000 2.100 N VAPA n/a
10 TRCN0000380815 ACCACACAGTGTTTCACTTAA pLKO_005 859 CDS 100% 13.200 7.920 N VAPA n/a
11 TRCN0000293262 TTTGTGTGTACAGCGTCATAT pLKO_005 1232 3UTR 100% 13.200 7.920 N VAPA n/a
12 TRCN0000381927 TTTGTGTGTACAGCGTCATAT pLKO_005 1232 3UTR 100% 13.200 7.920 N Vapa n/a
13 TRCN0000380105 ACCGAAACAAGGAAACTAATG pLKO_005 884 CDS 100% 10.800 6.480 N VAPA n/a
14 TRCN0000093613 ACAGATGTAGTCACTACAAAT pLKO.1 329 CDS 100% 13.200 6.600 Y Vapa n/a
15 TRCN0000317486 ACAGATGTAGTCACTACAAAT pLKO_005 329 CDS 100% 13.200 6.600 Y Vapa n/a
16 TRCN0000341259 TGGATTCTTTCTAGGGAAATT pLKO_005 1096 CDS 100% 13.200 6.600 Y Mospd4 n/a
17 TRCN0000382165 AGATTTGTTTACCTACCATTT pLKO_005 1180 3UTR 100% 10.800 5.400 Y Vapa n/a
18 TRCN0000029130 GCGAAATCCATCGGATAGAAA pLKO.1 358 CDS 100% 5.625 2.813 Y VAPA n/a
19 TRCN0000293261 GCGAAATCCATCGGATAGAAA pLKO_005 358 CDS 100% 5.625 2.813 Y VAPA n/a
20 TRCN0000162985 GAGACAAGGTTTCACCATGTT pLKO.1 4131 3UTR 100% 4.950 2.475 Y LINC00336 n/a
21 TRCN0000029132 CTTGTTGTAATTGCAGCCATT pLKO.1 1070 CDS 100% 4.050 2.025 Y VAPA n/a
22 TRCN0000029131 GCCCTTTGACTATGATCCGAA pLKO.1 484 CDS 100% 2.640 1.320 Y VAPA n/a
23 TRCN0000155836 CCCAAAGTGCTGGGATTACAA pLKO.1 4195 3UTR 100% 5.625 2.813 Y KLHL30 n/a
24 TRCN0000141025 CCCAAAGTGCTGGGATTACTT pLKO.1 4195 3UTR 100% 5.625 2.813 Y EID2B 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_003574.6, 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_11349 pDONR223 100% 80.6% 80.6% None 1_21del;417_551del;868_882del n/a
2 ccsbBroad304_11349 pLX_304 0% 80.6% 80.6% V5 1_21del;417_551del;868_882del n/a
3 TRCN0000492044 ATTCCAACAAAGTTCTAGCTCCCC pLX_317 56.1% 80.6% 80.6% V5 1_21del;417_551del;868_882del n/a
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