Transcript: Human XM_024452190.1

PREDICTED: Homo sapiens RNA binding fox-1 homolog 2 (RBFOX2), transcript variant X23, mRNA.

Source:
NCBI, updated 2019-09-08
Taxon:
Homo sapiens (human)
Gene:
RBFOX2 (23543)
Length:
9380
CDS:
2794..3921

Additional Resources:

NCBI RefSeq record:
XM_024452190.1
NBCI Gene record:
RBFOX2 (23543)

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.

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shRNA constructs matching this transcript with 100% SDR[?] match

This list includes all shRNAs that have a perfect SDR[?] match to Human XM_024452190.1, 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 TRCN0000294132 AGACATTAGGAGCCGATAAAT pLKO_005 4263 3UTR 100% 15.000 21.000 N RBFOX2 n/a
2 TRCN0000294044 GTATATGGTCCGGAGTTATAT pLKO_005 3370 CDS 100% 15.000 21.000 N RBFOX2 n/a
3 TRCN0000306861 TTGGCGCTGTGGCGAGTTTAT pLKO_005 3856 CDS 100% 13.200 18.480 N RBFOX2 n/a
4 TRCN0000294042 GCCGCTTACAGTGACGGTTAT pLKO_005 3777 CDS 100% 10.800 15.120 N RBFOX2 n/a
5 TRCN0000074544 CGGGTTCGTAACTTTCGAGAA pLKO.1 3192 CDS 100% 4.050 5.670 N RBFOX2 n/a
6 TRCN0000311693 CGGGTTCGTAACTTTCGAGAA pLKO_005 3192 CDS 100% 4.050 5.670 N RBFOX2 n/a
7 TRCN0000074545 GCATCCAGCTTTCAAGCAGAT pLKO.1 3394 CDS 100% 4.050 2.835 N RBFOX2 n/a
8 TRCN0000074546 CATATGCAAATGGTTGGAAAT pLKO.1 3329 CDS 100% 0.000 0.000 N RBFOX2 n/a
9 TRCN0000074547 CCATATGCAAATGGTTGGAAA pLKO.1 3328 CDS 100% 0.000 0.000 N RBFOX2 n/a
10 TRCN0000074543 CCTCACTATGTTCTTTGAATA pLKO.1 4068 3UTR 100% 13.200 7.920 N RBFOX2 n/a
11 TRCN0000181002 GAGACCCACCTTGCTCATAAA pLKO.1 657 5UTR 100% 13.200 6.600 Y RPL41 n/a
12 TRCN0000345612 ATGAGGCAGAGGTCCAAGTAA pLKO_005 480 5UTR 100% 5.625 2.813 Y Rpl41 n/a
13 TRCN0000431724 ACAGGAGCAGAAACATGGAAT pLKO_005 529 5UTR 100% 4.950 2.475 Y RPL41 n/a
14 TRCN0000442643 AGGCAGAGGTCCAAGTAAACC pLKO_005 483 5UTR 100% 4.950 2.475 Y RPL41 n/a
15 TRCN0000425539 CAAGTAAACCGCTAGCTTGTT pLKO_005 494 5UTR 100% 4.950 2.475 Y RPL41 n/a
16 TRCN0000182992 CTTGTCTCAATGGATCTAGAA pLKO.1 605 5UTR 100% 4.950 2.475 Y RPL41 n/a
17 TRCN0000446752 GGGATGCTGGTACAAGTTGTG pLKO_005 561 5UTR 100% 4.050 2.025 Y RPL41 n/a
18 TRCN0000439430 GTTGTGGGACTGCATGCTACT pLKO_005 576 5UTR 100% 4.050 2.025 Y RPL41 n/a
19 TRCN0000180882 GAAGAAAGATGAGGCAGAGGT pLKO.1 472 5UTR 100% 2.640 1.320 Y RPL41 n/a
20 TRCN0000329146 TGAGGCAGAGGTCCAAGTAAG pLKO_005 481 5UTR 100% 10.800 5.400 Y Rpl41 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_024452190.1, 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_02790 pDONR223 100% 91.1% 72.8% None (many diffs) n/a
2 ccsbBroad304_02790 pLX_304 0% 91.1% 72.8% V5 (many diffs) n/a
3 ccsbBroadEn_11745 pDONR223 100% 85.4% 67.3% None (many diffs) n/a
4 ccsbBroad304_11745 pLX_304 0% 85.4% 67.3% V5 (many diffs) n/a
5 TRCN0000478244 AAGGTTCGACCCGCACGGCTGATA pLX_317 24.7% 85.4% 67.3% V5 (many diffs) n/a
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