RetrogeneDB ID: retro_pabe_1491

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:29065544..29065844(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGRMC1
• Ensembl ID: ENSPPYG00000020666
• Aliases: None
• Description: Membrane-associated progesterone receptor component 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5RED0]

Sequence

>retro_pabe_1491
GGCAAGGTGTTCAGTGTGACCAGAGGTTGCAAGTTCCAAGGGCCAAGGGGCTGCACAGGATCTTTGCTGAAGAGATACAT
CCAGGGGCACTGCCACATTTTGCCTGGATAAGGGAGCACTGCAGGACAAGCATGATGACCTTTCTGACCTCCCTCCTGCC
CAGGAGGAGACCCTGAGTGACTGGGCCTCTCAGTTCACGTTCAAGTATTCTCACCTGGATAAACTGCTGAAGGAGGGGAG
GTACCCACTGTGGATTCAGATAAGGAAGAACCAAAAGATGAGAATGTACAGAAAAATGAT

Alignment

ORF - retro_pabe_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.19 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKVFDVTKGRKFYGPEGPYG-VFAG-RDASRGLATFCLDKEALKDEYDDLSDLTAAQQETLSDWESQFTF
          GKVF.VT.G.KF.GP.G..G..FA..RD.SRG.ATFCLDK.AL.D..DDLSDL..AQ.ETLSDW.SQFTF
Retrocopy GKVFSVTRGCKFQGPRGCTG<IFAE<RDTSRGTATFCLDKGALQDKHDDLSDLPPAQEETLSDWASQFTF

Parental  KYHHVGKLLKE-GEEPTVYSDEEEPKDESARKND
          KY.H..KLLKE.GE.PTV.SD.EEPKDE...KND
Retrocopy KYSHLDKLLKE<GEVPTVDSDKEEPKDENVQKND

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	68.73 RPM
SRP007412_cerebellum	0.00 RPM	63.48 RPM
SRP007412_heart	0.00 RPM	7.35 RPM
SRP007412_kidney	0.00 RPM	132.09 RPM
SRP007412_liver	0.00 RPM	190.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1491 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1491 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1824
Gorilla gorilla	retro_ggor_2170
Macaca mulatta	retro_mmul_1252

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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,