TABLE 2.
Top 22 XIST-like lncRNAs from GENCODE v43
| Transcript ID | Gene name | Transcript length | Tot_RNA | chrom_RNA | cyt_RNA | %_chrom | Rep.A | Rep.F | Rep.B1 | Rep.B2 | Rep.D | Rep.E | SUM |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ENST00000626826.1 | HELLPAR | 205,012 | 0.117 | 1.955 | 0.008 | 99.5 | 16 | 3 | 0 | 0 | 2 | 137 | 158 |
| ENST00000624628.1 | ENSG00000279072 | 24,137 | 0.002 | 0.004 | 0.001 | 70.3 | 0 | 0 | 0 | 35 | 0 | 0 | 35 |
| ENST00000429829.6 | XIST | 19,245 | 4.83 | 403.8 | 0.776 | 99.8 | 3 | 3 | 1 | 1 | 12 | 14 | 34 |
| ENST00000501122.2 | NEAT1 | 22,743 | 3.82 | 884.2 | 3.867 | 99.6 | 2 | 5 | 0 | 0 | 1 | 20 | 28 |
| ENST00000623075.1 | ENSG00000280383 | 23,112 | 0.008 | 0.051 | 0.098 | 33.8 | 3 | 0 | 3 | 3 | 0 | 16 | 25 |
| ENST00000568752.1 | ENSG00000261200 | 3971 | 0.000 | 0.245 | 0.005 | 97.5 | 5 | 0 | 0 | 3 | 5 | 5 | 18 |
| ENST00000587762.2 | MIR23AHG | 19,049 | 0.750 | 12.83 | 1.334 | 90.6 | 2 | 1 | 5 | 6 | 0 | 2 | 16 |
| ENST00000624209.1 | ENSG00000279036 | 3578 | 0.000 | 0.000 | 0.000 | NA | 3 | 0 | 5 | 5 | 0 | 1 | 14 |
| ENST00000609439.2 | ENSG00000291208 | 10,247 | 0.072 | 3.426 | 0.290 | 92.2 | 1 | 0 | 1 | 12 | 0 | 0 | 14 |
| ENST00000597346.1 | KCNQ1OT1 | 91,667 | 0.793 | 41.87 | 0.084 | 99.8 | 1 | 2 | 2 | 6 | 1 | 2 | 14 |
| ENST00000648200.2 | LINC00632 | 21,234 | 0.000 | 0.000 | 0.000 | NA | 1 | 0 | 0 | 0 | 1 | 12 | 14 |
| ENST00000458178.2 | PPM1F-AS1 | 37,852 | 0.000 | 0.000 | 0.000 | NA | 1 | 0 | 2 | 8 | 1 | 2 | 14 |
| ENST00000605862.6 | ENSG00000242588 | 17,286 | 2.556 | 69.70 | 1.624 | 97.7 | 1 | 0 | 2 | 7 | 0 | 2 | 12 |
| ENST00000604411.1 | TSIX | 37,027 | 0.003 | 0.267 | 0.000 | 99.6 | 1 | 4 | 1 | 0 | 0 | 6 | 12 |
| ENST00000624919.1 | ENSG00000280434 | 14,262 | 0.000 | 1.185 | 0.006 | 99.4 | 1 | 2 | 0 | 4 | 0 | 4 | 11 |
| ENST00000671643.1 | ENSG00000286288 | 4575 | 0.000 | 0.000 | 0.000 | NA | 2 | 0 | 4 | 1 | 2 | 2 | 11 |
| ENST00000610177.1 | LINC02604 | 3441 | 0.085 | 22.85 | 1.329 | 94.5 | 2 | 0 | 0 | 6 | 0 | 3 | 11 |
| ENST00000635449.1 | PRNCR1 | 12,727 | 0.000 | 0.080 | 0.001 | 97.5 | 0 | 1 | 0 | 0 | 0 | 10 | 11 |
| ENST00000657488.1 | ENSG00000286379 | 4878 | 0.032 | 4.110 | 0.095 | 97.7 | 0 | 0 | 6 | 2 | 0 | 2 | 10 |
| ENST00000622550.2 | ENSG00000290535 | 7213 | 0.084 | 4.137 | 0.145 | 96.6 | 1 | 0 | 2 | 7 | 0 | 0 | 10 |
| ENST00000506640.3 | ENSG00000291215 | 6469 | 0.248 | 25.48 | 0.825 | 96.9 | 2 | 0 | 1 | 7 | 0 | 0 | 10 |
| ENST00000665286.1 | RENO1 | 6784 | 0.342 | 5.097 | 0.383 | 93.0 | 4 | 0 | 4 | 1 | 1 | 0 | 10 |
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“tot_RNA,” total/ribosome-depletion RNA-seq data; “chrom_RNA,” chromatin fraction RNA-seq data; “cyt_RNA,” cytosolic fraction RNA-seq data; all RNA-seq data are displayed in TPM units and were collected from K562 cells as part of the ENCODE project (Dunham et al. 2012). “%_chrom,” 100*[chrom_RNA_TPM]/[chrom_RNA_TPM + cyt_RNA_TPM + 0.0001]. “Rep.[A–E],” count of significant hits to each XIST repeat when analyzing the 500 nt chunks of each listed lncRNA. “SUM” sum of counts in “Rep.[A–E]” columns.
