RetrogeneDB ID: retro_rnor_1461

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:45084628..45085059(-)
• Located in intron of: ENSRNOG00000013152

Retrocopy information

• Ensembl ID: ENSRNOG00000027022
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pgrmc1
• Ensembl ID: ENSRNOG00000012786
• Aliases: Pgrmc1, 25-Dx, 25Dx, MPR, VEMA
• Description: Membrane-associated progesterone receptor component 1 [Source:UniProtKB/Swiss-Prot;Acc:P70580]

Sequence

>retro_rnor_1461
GGTGCCAGTGGCGACAACGACGACGATGGCCGCCCCCGCTGCCCCGCCTCAAGCCGCGTGACTTCACCCCTGCCGAACTG
AGGCGTTACGATGGCGTCCAGGACCCGCGCATTCTTATGGCCATCAACCGCAAGGTGTTCGACGTGACCAAAGGCTGCAA
GTTCTACGGGCCGGAGGGGCCATACGGGGTCTTTGCTGTTAGAGATGCATCCAGGGGCCTTGCCACATTTTGCCTGGACA
AAGAAGCACTGAAGGATGTGTATGATGACCTTTCTGACCTCACTCCTGCCCAGCAGGAGACCCTGAATGACTGGGACTCT
CAGTTCACCTTCAAGTACCATCACGTGGGAAAACTGCTGAAGGAAGGGGAGGAGCCGACTGTGTACTCGGATGATGAAGA
ACCAAAAGATGAGACTGCCCGGAAGAGTGAC

Alignment

ORF - retro_rnor_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.17 %
• Parental protein coverage: 73.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GASGDNDDDE-PPPLPRLKPRDFTPAELRRYDGVQDPRILMAINGKVFDVTKGRKFYGPEGPYGVFAGRD
          GASGDNDDD..PPPLPRLKPRDFTPAELRRYDGVQDPRILMAIN.KVFDVTKG.KFYGPEGPYGVFA.RD
Retrocopy GASGDNDDDG<PPPLPRLKPRDFTPAELRRYDGVQDPRILMAINRKVFDVTKGCKFYGPEGPYGVFAVRD

Parental  ASRGLATFCLDKEALKDEYDDLSDLTPAQQETLNDWDSQFTFKYHHVGKLLKEGEEPTVYSDDEEPKDEA
          ASRGLATFCLDKEALKD.YDDLSDLTPAQQETLNDWDSQFTFKYHHVGKLLKEGEEPTVYSDDEEPKDE.
Retrocopy ASRGLATFCLDKEALKDVYDDLSDLTPAQQETLNDWDSQFTFKYHHVGKLLKEGEEPTVYSDDEEPKDET

Parental  ARKSD
          ARKSD
Retrocopy ARKSD

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	0.29 RPM	162.49 RPM
SRP017611_kidney	0.14 RPM	297.69 RPM
SRP017611_liver	0.20 RPM	583.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1461 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018372	1 retrocopy	retro_cfam_1237,
Homo sapiens	ENSG00000101856	1 retrocopy	retro_hsap_1824,
Macaca mulatta	ENSMMUG00000014466	1 retrocopy	retro_mmul_1252,
Nomascus leucogenys	ENSNLEG00000014842	1 retrocopy	retro_nleu_2797,
Pongo abelii	ENSPPYG00000020666	1 retrocopy	retro_pabe_1491,
Rattus norvegicus	ENSRNOG00000012786	1 retrocopy	retro_rnor_1461 ,
Ictidomys tridecemlineatus	ENSSTOG00000024047	1 retrocopy	retro_itri_1619,