RetrogeneDB ID: retro_rnor_2035

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:7064532..7065570(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000025214
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gpd1l
• Ensembl ID: ENSRNOG00000026455
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like protein [Source:RefSeq peptide;Acc:NP_001178814]

Sequence

>retro_rnor_2035
CCCCTGAAAGTGAGCATCGTGGGTTCAGGGAACTGGGCGTCAGCTGTTTCAAAAATCATTGGGAACAATGTGAAGACCAC
CAAGAAGTTCGCTTCCCCGGTCAAGATGTGGGTATTTGAAGAGATCGTCAATGGGAGGAAGCTGACAGACATCATCAACA
CTGATCACGAAAACGTAAAGTACCTTCCCGGATACAGGCTGCCCGAGAATGTGATAGCTACTCCAAGTCTCAGCCAGGCT
GTGCAGGACGCAGACCTGCTGGTGTTTGCTTTCCCACACCAGTTCATTCGAAAAATCTGTGATGAACTCGCTGAAGTGGT
GCCCAGGAAAGCCCGAGGCCTCACCCTCATCAAAGGCATAGACGAAGGCCCCGAGAGCCTGAAGCTTATCTCTGACATCA
TCCGAGAGAAGGTGAACATAGATGTCAGCGTGCTGATGGGGGCCAACTTAGCCAATGAGGTGGCTGCAGAGCAGTTCTGC
GAGACCACCATTGGCAGCAAGGTGCTGCAGAACGGCCTTCTCTTCAAAGAGCTGTTTCAGACCCCCAACTTCCGAGTCAC
TGTGGTTGAAGATCCAGACACGGTGGAGCTGTGCGGAGCTCTAAAGAACATTGTCGCCATGGGGTCCGGGTTCTGCGACA
GCTTCTGTTGTGGAAACAGCACCAAGGCTGCTGTCATCCGCCTGGGCCTCATGGAGATGATTTCTTTTGTCAGGACCTTC
TCCAAGGGCCAAGTGTCCATAGCCACTTTCCTGGAGAGCTGCGGGGTGGCTGACCTCATCAGTACCTGCTACGGGGGGCG
GAACCGAAAGGTAGCGGAAGCCTTCGCCAGGACAGGAAAAAGCCTTGAGGAGTTGGAGAAGGAGATGCTGAAGGGACAGA
AGCTGCAAGGGCCACACACCTCTGCCCAGGTGTACCGCATCCTCAAGCAGAAGGGGCTGCTGGACAAGTTTCCACTGTTC
ACAGTTGTGTATCAAATCTGTTACGAGGGCAGAGCAGTTACCGAGCTGATACCCTGTCTACAGAACCACCCAGAGCAC

Alignment

ORF - retro_rnor_2035 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 98.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLKVCIVGSGNWGSAVAKIIGSNVKNLQKFSSTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPEN
          PLKV.IVGSGNW.SAV.KIIG.NVK...KF.S.VKMWVFEE.VNGRKLTDIIN.DHENVKYLPG..LPEN
Retrocopy PLKVSIVGSGNWASAVSKIIGNNVKTTKKFASPVKMWVFEEIVNGRKLTDIINTDHENVKYLPGYRLPEN

Parental  VVAVPNLGEAVQDADLLVFVIPHQFIHKICDEITGRVPKKAVGITLIKGIDEGPDGLKLISDIIREKMGI
          V.A.P.L..AVQDADLLVF..PHQFI.KICDE....VP.KA.G.TLIKGIDEGP..LKLISDIIREK..I
Retrocopy VIATPSLSQAVQDADLLVFAFPHQFIRKICDELAEVVPRKARGLTLIKGIDEGPESLKLISDIIREKVNI

Parental  DISVLMGANIASEVAAEKFCETTIGSKVLQNGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAVGAG
          D.SVLMGAN.A.EVAAE.FCETTIGSKVLQNGLLFKEL.QTPNFR.TVV.D.DTVELCGALKNIVA.G.G
Retrocopy DVSVLMGANLANEVAAEQFCETTIGSKVLQNGLLFKELFQTPNFRVTVVEDPDTVELCGALKNIVAMGSG

Parental  FCDGLCCGDNTKAAVIRLGLMEMIAFAKIFCKGQVSTATFLESCGVADLITTCYGGRNRKVAEAFARTGK
          FCD..CCG..TKAAVIRLGLMEMI.F...F.KGQVS.ATFLESCGVADLI.TCYGGRNRKVAEAFARTGK
Retrocopy FCDSFCCGNSTKAAVIRLGLMEMISFVRTFSKGQVSIATFLESCGVADLISTCYGGRNRKVAEAFARTGK

Parental  TIEELEKELLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYEGRPVTQMLSCLQSHPEH
          ..EELEKE.L.GQKLQGP.TSA.VYRILKQKGLLDKFPLFT.VYQICYEGR.VT....CLQ.HPEH
Retrocopy SLEELEKEMLKGQKLQGPHTSAQVYRILKQKGLLDKFPLFTVVYQICYEGRAVTELIPCLQNHPEH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	82.03 RPM
SRP017611_kidney	0.00 RPM	105.58 RPM
SRP017611_liver	0.00 RPM	14.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2035 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2035 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2552

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035 , retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,