Table 3.
Beaver noncoding contigs that are probable orthologs of known lncRNAs or noncoding transcripts
| Symbol; annotation | Contig | Species with ortholog hits | Human Ensembl Gene ID | BLASTn annotation | E | %ID | nt |
|---|---|---|---|---|---|---|---|
| AC037459.2; (antisense to CCAR2) | Ccan_OSU1_lncRNA_contig74544.1 | Homo sapiens | ENSG00000253200 | CCAR2 lncRNA (cell cycle and apoptosis regulator 2) | 8.0⨉10−46 | 89 | 155 |
| AC019068.1; antisense | Ccan_OSU1_lncRNA_contig10709.1 | Homo sapiens | ENSG00000233611 | AC079135.1 gene, antisense lncRNA (TPA - predicted) | 2.4⨉10−12 | 77.6 | 143 |
| AC083843.1 | Ccan_OSU1_lncRNA_contig47288.1 | Homo sapiens | ENSG00000253433 | AC083843.1 gene, lincRNA (TPA - predicted) | 7.7⨉10−13 | 88.4 | 69 |
| AC095055.1 (antisense to SH3D19) | Ccan_OSU1_lncRNA_contig41532.1 | Homo sapiens | ENSG00000270681 | SH3D19 antisense noncoding RNA (SH3 domain containing 19) | 8.1⨉10− 58 | 82.9 | 274 |
| AC116667.1; (antisense to ZFHX3) | Ccan_OSU1_lncRNA_contig71613.1 | Homo sapiens | ENSG00000271009 | ZFHX3 antisense (zinc finger homeobox 3) | 1.8⨉10−47 | 83.6 | 231 |
| AL161747.2; (antisense to SALL2) | Ccan_OSU1_lncRNA_contig44345.1 | Homo sapiens | ENSG00000257096 | SALL2 lncRNA (spalt-like transcription factor 2) | 7.5⨉10−68 | 84.4 | 288 |
| AP000233.2 | Ccan_OSU1_lncRNA_contig22249.1 | Homo sapiens | ENSG00000232512 | AP000233.2 gene lincRNA (TPA - predicted) | 9.0⨉10−5 | 100 | 31 |
| AP003068.1; (antisense to VPS51) | Ccan_OSU1_lncRNA_contig24716.1 | Homo sapiens, Mus musculus, Bos taurus | ENSG00000254501 | VPS51 antisense (vacuolar protein sorting 51) | 0 | 93.2 | 438 |
| AP003068.1; (antisense to VPS51) | Ccan_OSU1_lncRNA_contig55707.1 | Mus musculus, Homo sapiens, Gallus gallus | ENSG00000254501 | VPS51 antisense/reverse strand (vacuolar protein sorting 51) | 1.7⨉10−83 | 92 | 226 |
| CTA-204B4.6† | Ccan_OSU1_lncRNA_contig29141.1 | Homo sapiens | ENSG00000259758 | CTA-204B4.6 gene lincRNA (TPA - predicted) | 6.2⨉10− 120 | 83.5 | 491 |
| CTA-204B4.6 | Ccan_OSU1_lncRNA_contig30023.1 | Homo sapiens | ENSG00000259758 | CTA-204B4.6 gene lincRNA (TPA - predicted) | 2.1⨉10− 129 | 94.5 | 308 |
| DNM3OS; (antisense to DNM3) | Ccan_OSU1_lncRNA_contig78034.1 | Homo sapiens; various primates | ENSG00000230630 | DNM3OS (DNM3 opposite strand/antisense RNA) lncRNA | 3.4⨉10−69 | 89.8 | 216 |
| GNB4; lncRNA isoform* | Ccan_OSU1_lncRNA_contig55083.1 | Homo sapiens | ENSG00000114450 | GNB4 (guanine nucleotide binding protein (G protein), beta polypeptide 4) | 6.4⨉10−38 | 78.8 | 287 |
| AC007038.2; (antisense to KANSL1L) | Ccan_OSU1_lncRNA_contig54664.1 | Homo sapiens, Mus musculus | ENSG00000272807 | KANSL1L antisense transcript (KAT8 regulatory NSL complex subunit 1-like) | 1.1⨉10−40 | 92 | 125 |
| KCNA3; noncoding isoform | Ccan_OSU1_lncRNA_contig27553.1 | Homo sapiens, Mus musculus | ENSG00000177272 | KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3) | 2.3⨉10− 139 | 85.5 | 502 |
| KCNA3; noncoding isoform | Ccan_OSU1_lncRNA_contig29471.1 | Homo sapiens | ENSG00000177272 | KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3) | 1.8⨉10−70 | 78.7 | 475 |
| KCNA3; noncoding isoform | Ccan_OSU1_lncRNA_contig79757.1 | Homo sapiens | ENSG00000177272 | KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3) | 7.6⨉10−31 | 80.2 | 197 |
| KCNA3; noncoding isoform | Ccan_OSU1_lncRNA_contig81530.1 | Homo sapiens, Mus musculus | ENSG00000177272 | KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3) | 7.1⨉10−61 | 87.7 | 211 |
| LINC01355 | Ccan_OSU1_lncRNA_contig54147.1 | Homo sapiens | ENSG00000261326 | LINC01355 lncRNA | 1.0⨉10− 85 | 87.5 | 295 |
| LMLN; noncoding isoform* | Ccan_OSU1_lncRNA_contig28300.1 | Homo sapiens | ENSG00000185621 | LMLN (leishmanolysin-like (metallopeptidase M8 family) | 3.1⨉10− 73 | 80.4 | 414 |
| MEG3 | Ccan_OSU1_lncRNA_contig11359.1 | Homo sapiens, Mus musculus, Pongo abelii | ENSG00000214548 | MEG3 lncRNA (maternally expressed 3) | 1.6⨉10− 123 | 93 | 313 |
| MEG3 | Ccan_OSU1_lncRNA_contig30419.1 | Homo sapiens, Pongo abelii | ENSG00000214548 | MEG3 lncRNA (maternally expressed 3) | 7.6⨉10− 124 | 93 | 313 |
| MEG3 | Ccan_OSU1_lncRNA_contig6442.1 | Homo sapiens, Mus musculus, Pongo abelii | ENSG00000214548 | MEG3 lncRNA (maternally expressed 3) | 2.2⨉10−123 | 93 | 313 |
| N4BP2L2-IT2* | Ccan_OSU1_lncRNA_contig81871.1 | Homo sapiens | ENSG00000281026 | N4BP2L2-IT2 lncRNA (N4BPL2 intronic transcript 2) | 2.2⨉10−6 | 76.2 | 130 |
| NIPBL-DT | Ccan_OSU1_lncRNA_contig25986.1 | Homo sapiens | ENSG00000285967 | NIPBL lncRNA bidirectional promoter (Nipped-B homolog) | 3.6⨉10−38 | 80.9 | 225 |
| PDK3; noncoding isoform* | Ccan_OSU1_lncRNA_contig72478.1 | Homo sapiens | ENSG00000067992 | PDK3 (pyruvate dehydrogenase kinase, isozyme 3) | 1.8⨉10−37 | 84.2 | 171 |
| RASSF3; noncoding isoform* | Ccan_OSU1_lncRNA_contig10200.1 | Homo sapiens | ENSG00000153179 | RASSF3 (Ras associated (RalGDS/AF-6) domain family member 3) | 0 | 83.2 | 963 |
| RASSF3; noncoding isoform* | Ccan_OSU1_lncRNA_contig10200.2 | Homo sapiens | ENSG00000153179 | RASSF3 (Ras associated (RalGDS/AF-6) domain family member 3) | 0 | 83.3 | 962 |
| AC098818.2†; (antisense to BMP2K) | Ccan_OSU1_lncRNA_contig59404.1 | Homo sapiens | ENSG00000260278 | RP11-109G23.3 gene, antisense lncRNA | 4.5⨉10−59 | 83.3 | 275 |
| TRIM56; sense overlapping | Ccan_OSU1_lncRNA_contig18315.1 | Homo sapiens | ENSG00000169871 | RP11-395B7.7 gene, sense overlapping lncRNA (TPA - predicted) | 4.7⨉10−28 | 72.8 | 519 |
| RP11-395B7.7 | Ccan_OSU1_lncRNA_contig47935.1 | Homo sapiens | ENSG00000260336 | RP11-395B7.7 gene, sense overlapping lncRNA (TPA - predicted) | 9.7⨉10−22 | 73.9 | 284 |
| AC090948.1 | Ccan_OSU1_lncRNA_contig29838.1 | Homo sapiens | ENSG00000271964 | RP11-415F23.2 gene, antisense lncRNA (TPA - predicted) | 1.5⨉10−26 | 93.3 | 89 |
| AL591848.4† | Ccan_OSU1_lncRNA_contig59344.1 | Homo sapiens | ENSG00000260855 | RP11-439E19.10 gene, antisense lncRNA (TPA - predicted) | 4.9⨉10−4 | 96.9 | 32 |
| AC022893.2 | Ccan_OSU1_lncRNA_contig76877.1 | Homo sapiens | ENSG00000260838 | RP11-531A24.3 gene, lincRNA (TPA - predicted) | 3.6⨉10−39 | 81.4 | 226 |
| AL355488.1 (antisense to SLC16A4) | Ccan_OSU1_lncRNA_contig17784.1 | Homo sapiens | ENSG00000273373 | RP5-1074 L1.4 gene, antisense lncRNA (TPA - predicted) | 1.0⨉10−44 | 89.9 | 149 |
| THRB-AS1; (antisense to THRB) | Ccan_OSU1_lncRNA_contig53102.1 | Homo sapiens | ENSG00000228791 | THRB antisense/reverse strand (thyroid hormone receptor, beta) | 6.8⨉10−18 | 80.9 | 136 |
| TINCR; lncRNA isoform | Ccan_OSU1_lncRNA_contig14850.1 | Homo sapiens | ENSG00000223573 | TINCR lncRNA (tissue differentiation-inducing non-protein coding RNA) | 4.1⨉10−44 | 82.2 | 225 |
| TUG1; lncRNA isoform | Ccan_OSU1_lncRNA_contig6874.1 | Mus musculus | ENSG00000253352 | TUG1 lncRNA (taurine upregulated gene 1) | 6.2⨉10−79 | 79.9 | 448 |
| UBR5; lncRNA isoform* | Ccan_OSU1_lncRNA_contig10406.1 | Homo sapiens, Bos taurus | ENSG00000104517 | UBR5 (ubiquitin protein ligase E3 component n-recognin 5) | 0 | 82.9 | 977 |
| XIST | Ccan_OSU1_lncRNA_contig185.1 | Homo sapiens, Mus musculus | ENSG00000229807 | XIST lncRNA (X inactive specific transcript) | 3.1⨉10− 136 | 79.7 | 772 |
E, the E-value for the highest-scoring BLASTn match; %ID, percent identity between the contig and matching query sequence, by BLASTn; nt, length of match (nt); E-value of “0” means that E < 2.23 × 10− 308. Columns as follows: “Symbol”, Human Gene Nomenclature Committee gene symbol; “annotation”, classification of the lncRNA transcript type if it is not an obligate lncRNA gene or if it is antisense to a protein-coding gene (i. entries with an asterisk after the annotation denote noncoding transcript contigs whose orthologs are potential noncoding isoforms; see Methods; ii. entries with a dagger after the annotate denote transcripts which have new BLASTn annotations for beaver, as of November 18, 2019); “Contig,”, the name of the transcript contig; “Species”, the species in which orthologs of the contig were detected by sequence similarity; Ensembl Gene ID, the Ensembl gene identifier of the putative human ortholog; “BLASTn annotation”, the annotation of the BLASTn hit corresponding to the statistics in the last three columns (E, %ID, nt)