RetrogeneDB ID: retro_rnor_1878

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:38629358..38629644(-)
• Located in intron of: ENSRNOG00000027596

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Plac8
• Ensembl ID: ENSRNOG00000002217
• Aliases: None
• Description: placenta-specific gene 8 protein [Source:RefSeq peptide;Acc:NP_001101823]

Sequence

>retro_rnor_1878
ATGGCTCAGGCACCAACAGTCATCATGACTCAACCTGGATTTGTTCATGCTCCCCAAAATTCCAGCTGGCAGAGCAGCCT
GTGTGGTTGTTTCAGTGACCGCAGGATCTGCTTCTGTGGGACCTTTTGCTTCACTATGGCTTGGATGTTGAGTGGCAGCT
GACATGAATGAATGTTGTTTGGGTGGAACAATGGTGGCAAGGAGGACTCTCTCTCCCCCAGTACACATTCCTGGATCTAT
TTGTGATGAGTACATAGATACCTTCTCCTGTCCTGTTTGTTGTGTG

Alignment

ORF - retro_rnor_1878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.13 %
• Parental protein coverage: 85.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQAATVIVTQPGFVRAPQNSNWQTSLCDCFSDCGVCLCGTFCFTC-LGCQVAADMNECCLCGTTVAMRT
          MAQA.TVI.TQPGFV.APQNS.WQ.SLC.CFSD...C.CGTFCFT..LGC.VAADMNECCL.GT.VA.RT
Retrocopy MAQAPTVIMTQPGFVHAPQNSSWQSSLCGCFSDRRICFCGTFCFTM>LGC*VAADMNECCLGGTMVARRT

Parental  LYRTRYGIPGSICDDYMVTLFCPVCSV
          L......IPGSICD.Y..T..CPVC.V
Retrocopy LSPPVH-IPGSICDEYIDTFSCPVCCV

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	0.50 RPM
SRP017611_kidney	0.07 RPM	17.17 RPM
SRP017611_liver	0.00 RPM	2.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1878 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145287	1 retrocopy	retro_hsap_1165,
Gorilla gorilla	ENSGGOG00000007464	1 retrocopy	retro_ggor_910,
Monodelphis domestica	ENSMODG00000019309	1 retrocopy	retro_mdom_950,
Mus musculus	ENSMUSG00000029322	1 retrocopy	retro_mmus_1051,
Otolemur garnettii	ENSOGAG00000017232	1 retrocopy	retro_ogar_714,
Pan troglodytes	ENSPTRG00000016226	1 retrocopy	retro_ptro_800,
Rattus norvegicus	ENSRNOG00000002217	2 retrocopies	retro_rnor_1489, retro_rnor_1878 ,