Skip to main content

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; 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

  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)
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us