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Table 3 Beaver noncoding contigs that are probable orthologs of known lncRNAs or noncoding transcripts

From: Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

Symbol; annotationContigSpecies with ortholog hitsHuman Ensembl Gene IDBLASTn annotationE%IDnt
AC037459.2; (antisense to CCAR2)Ccan_OSU1_lncRNA_contig74544.1Homo sapiensENSG00000253200CCAR2 lncRNA (cell cycle and apoptosis regulator 2)8.010−4689155
AC019068.1; antisenseCcan_OSU1_lncRNA_contig10709.1Homo sapiensENSG00000233611AC079135.1 gene, antisense lncRNA (TPA - predicted)2.410−1277.6143
AC083843.1Ccan_OSU1_lncRNA_contig47288.1Homo sapiensENSG00000253433AC083843.1 gene, lincRNA (TPA - predicted)7.710−1388.469
AC095055.1 (antisense to SH3D19)Ccan_OSU1_lncRNA_contig41532.1Homo sapiensENSG00000270681SH3D19 antisense noncoding RNA (SH3 domain containing 19)8.110− 5882.9274
AC116667.1; (antisense to ZFHX3)Ccan_OSU1_lncRNA_contig71613.1Homo sapiensENSG00000271009ZFHX3 antisense (zinc finger homeobox 3)1.810−4783.6231
AL161747.2; (antisense to SALL2)Ccan_OSU1_lncRNA_contig44345.1Homo sapiensENSG00000257096SALL2 lncRNA (spalt-like transcription factor 2)7.510−6884.4288
AP000233.2Ccan_OSU1_lncRNA_contig22249.1Homo sapiensENSG00000232512AP000233.2 gene lincRNA (TPA - predicted)9.010−510031
AP003068.1; (antisense to VPS51)Ccan_OSU1_lncRNA_contig24716.1Homo sapiens, Mus musculus, Bos taurusENSG00000254501VPS51 antisense (vacuolar protein sorting 51)093.2438
AP003068.1; (antisense to VPS51)Ccan_OSU1_lncRNA_contig55707.1Mus musculus, Homo sapiens, Gallus gallusENSG00000254501VPS51 antisense/reverse strand (vacuolar protein sorting 51)1.710−8392226
CTA-204B4.6†Ccan_OSU1_lncRNA_contig29141.1Homo sapiensENSG00000259758CTA-204B4.6 gene lincRNA (TPA - predicted)6.210− 12083.5491
CTA-204B4.6Ccan_OSU1_lncRNA_contig30023.1Homo sapiensENSG00000259758CTA-204B4.6 gene lincRNA (TPA - predicted)2.110− 12994.5308
DNM3OS; (antisense to DNM3)Ccan_OSU1_lncRNA_contig78034.1Homo sapiens; various primatesENSG00000230630DNM3OS (DNM3 opposite strand/antisense RNA) lncRNA3.410−6989.8216
GNB4; lncRNA isoform*Ccan_OSU1_lncRNA_contig55083.1Homo sapiensENSG00000114450GNB4 (guanine nucleotide binding protein (G protein), beta polypeptide 4)6.410−3878.8287
AC007038.2; (antisense to KANSL1L)Ccan_OSU1_lncRNA_contig54664.1Homo sapiens, Mus musculusENSG00000272807KANSL1L antisense transcript (KAT8 regulatory NSL complex subunit 1-like)1.110−4092125
KCNA3; noncoding isoformCcan_OSU1_lncRNA_contig27553.1Homo sapiens, Mus musculusENSG00000177272KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3)2.310− 13985.5502
KCNA3; noncoding isoformCcan_OSU1_lncRNA_contig29471.1Homo sapiensENSG00000177272KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3)1.810−7078.7475
KCNA3; noncoding isoformCcan_OSU1_lncRNA_contig79757.1Homo sapiensENSG00000177272KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3)7.610−3180.2197
KCNA3; noncoding isoformCcan_OSU1_lncRNA_contig81530.1Homo sapiens, Mus musculusENSG00000177272KCNA3 lncRNA (potassium voltage-gated channel, shaker-related subfamily, member 3)7.110−6187.7211
LINC01355Ccan_OSU1_lncRNA_contig54147.1Homo sapiensENSG00000261326LINC01355 lncRNA1.010− 8587.5295
LMLN; noncoding isoform*Ccan_OSU1_lncRNA_contig28300.1Homo sapiensENSG00000185621LMLN (leishmanolysin-like (metallopeptidase M8 family)3.110− 7380.4414
MEG3Ccan_OSU1_lncRNA_contig11359.1Homo sapiens, Mus musculus, Pongo abeliiENSG00000214548MEG3 lncRNA (maternally expressed 3)1.610− 12393313
MEG3Ccan_OSU1_lncRNA_contig30419.1Homo sapiens, Pongo abeliiENSG00000214548MEG3 lncRNA (maternally expressed 3)7.610− 12493313
MEG3Ccan_OSU1_lncRNA_contig6442.1Homo sapiens, Mus musculus, Pongo abeliiENSG00000214548MEG3 lncRNA (maternally expressed 3)2.210−12393313
N4BP2L2-IT2*Ccan_OSU1_lncRNA_contig81871.1Homo sapiensENSG00000281026N4BP2L2-IT2 lncRNA (N4BPL2 intronic transcript 2)2.210−676.2130
NIPBL-DTCcan_OSU1_lncRNA_contig25986.1Homo sapiensENSG00000285967NIPBL lncRNA bidirectional promoter (Nipped-B homolog)3.610−3880.9225
PDK3; noncoding isoform*Ccan_OSU1_lncRNA_contig72478.1Homo sapiensENSG00000067992PDK3 (pyruvate dehydrogenase kinase, isozyme 3)1.810−3784.2171
RASSF3; noncoding isoform*Ccan_OSU1_lncRNA_contig10200.1Homo sapiensENSG00000153179RASSF3 (Ras associated (RalGDS/AF-6) domain family member 3)083.2963
RASSF3; noncoding isoform*Ccan_OSU1_lncRNA_contig10200.2Homo sapiensENSG00000153179RASSF3 (Ras associated (RalGDS/AF-6) domain family member 3)083.3962
AC098818.2†; (antisense to BMP2K)Ccan_OSU1_lncRNA_contig59404.1Homo sapiensENSG00000260278RP11-109G23.3 gene, antisense lncRNA4.510−5983.3275
TRIM56; sense overlappingCcan_OSU1_lncRNA_contig18315.1Homo sapiensENSG00000169871RP11-395B7.7 gene, sense overlapping lncRNA (TPA - predicted)4.710−2872.8519
RP11-395B7.7Ccan_OSU1_lncRNA_contig47935.1Homo sapiensENSG00000260336RP11-395B7.7 gene, sense overlapping lncRNA (TPA - predicted)9.710−2273.9284
AC090948.1Ccan_OSU1_lncRNA_contig29838.1Homo sapiensENSG00000271964RP11-415F23.2 gene, antisense lncRNA (TPA - predicted)1.510−2693.389
AL591848.4†Ccan_OSU1_lncRNA_contig59344.1Homo sapiensENSG00000260855RP11-439E19.10 gene, antisense lncRNA (TPA - predicted)4.910−496.932
AC022893.2Ccan_OSU1_lncRNA_contig76877.1Homo sapiensENSG00000260838RP11-531A24.3 gene, lincRNA (TPA - predicted)3.610−3981.4226
AL355488.1 (antisense to SLC16A4)Ccan_OSU1_lncRNA_contig17784.1Homo sapiensENSG00000273373RP5-1074 L1.4 gene, antisense lncRNA (TPA - predicted)1.010−4489.9149
THRB-AS1; (antisense to THRB)Ccan_OSU1_lncRNA_contig53102.1Homo sapiensENSG00000228791THRB antisense/reverse strand (thyroid hormone receptor, beta)6.810−1880.9136
TINCR; lncRNA isoformCcan_OSU1_lncRNA_contig14850.1Homo sapiensENSG00000223573TINCR lncRNA (tissue differentiation-inducing non-protein coding RNA)4.110−4482.2225
TUG1; lncRNA isoformCcan_OSU1_lncRNA_contig6874.1Mus musculusENSG00000253352TUG1 lncRNA (taurine upregulated gene 1)6.210−7979.9448
UBR5; lncRNA isoform*Ccan_OSU1_lncRNA_contig10406.1Homo sapiens, Bos taurusENSG00000104517UBR5 (ubiquitin protein ligase E3 component n-recognin 5)082.9977
XISTCcan_OSU1_lncRNA_contig185.1Homo sapiens, Mus musculusENSG00000229807XIST lncRNA (X inactive specific transcript)3.110− 13679.7772
  1. 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)