RetrogeneDB ID: retro_pcap_239

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_204577:7..636(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGRMC2
• Ensembl ID: ENSPCAG00000002433
• Aliases: None
• Description: progesterone receptor membrane component 2 [Source:HGNC Symbol;Acc:16089]

Sequence

>retro_pcap_239
AGGTGGGTGATGATAGCGGTGGGTGATGGGGATGTGAAGTTAGTTACCCTGGGGAGTGGCAGCAATAGCAGCGGTGACGA
AGGCAGCCACAGTCCTGGAGGTGCGGGAGCGGCAGCTGAAGAGGGCAGCTGGGCGGCAGTGGTGTTGACGCTTCTGACCA
ACGGAGGGGAGATGCAGCTGTATGTGGTGCTGGTGGCACTTGGGCTGTGGGGGCCTAAAGACTGTGAGTGCGCTGGAGGC
TACAGGATATAAGTGCCCAGGCTGGGGTGGACAAGGAGAGTCCTGCCACCTCTCTGCCTCACATGAAGAAGTGGGACCTT
GGTTTGGAGCAGCTGCGCCAGTGTGAGGAGTCCAAAAACCTGTGTATCCTGTATGCGGTCAACGGAAAGTTTTTGATGTG
ACCGAGGGTAGCAAGGTCTACGGCCCTGGGGGTCCGTATGGAATATGTGCTGGTAGGGATGCCTCCAGAGGACTGGTAAT
GTTTTGTCTAGATAAAAACGCACTTCGAGATGAATATGATGATGTGTCAGATTCAAATGCCGTACAAACGGAGAGCGTTA
GAGAATAGAAATTGCAGAATTAAAGAAAAATATGATTATGTAGGCAGACTCCTAAAACCAGGAGAAGAG

Alignment

ORF - retro_pcap_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 85.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RWRAVMAAGDGDVKLGTLGSGSDSSSDGSSEIPGGAGATAEEGGWAAAALALLTGGGEMLLNVVLVALVL
          RW....A.GDGDVKL.TLGSGS.SS.D..S..PGGAGA.AEEG.WAA..L.LLT.GGEM.L.VVLVAL.L
Retrocopy RW-VMIAVGDGDVKLVTLGSGSNSSGDEGSHSPGGAGAAAEEGSWAAVVLTLLTNGGEMQLYVVLVALGL

Parental  -LGAYRLWMRWGRRGLGAGAGAGEESPAASLPRMKKRDFSLEQLRQYDGSNNPRILLAVNGK-VFDVTKG
          ..GA.RL..RW......A.AG...ESPA.SLP.MKK.D..LEQLRQ...S.N..IL.AVNGK.VFDVT.G
Retrocopy <VGA*RL*VRWRLQDISAQAGVDKESPATSLPHMKKWDLGLEQLRQCEESKNLCILYAVNGK<VFDVTEG

Parental  SKFYGPAGPYGIFAGRDASRGLATFCLDKDALRDEYDDLSDLNAVQMESVREWEMQ-FKEKYDYVGRLLK
          SK.YGP.GPYGI.AGRDASRGL..FCLDK.ALRDEYDD.SD.NAVQ.ESVRE...Q..KEKYDYVGRLLK
Retrocopy SKVYGPGGPYGICAGRDASRGLVMFCLDKNALRDEYDDVSDSNAVQTESVRE*KLQ>IKEKYDYVGRLLK

Parental  PGEE
          PGEE
Retrocopy PGEE

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_239 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003328	1 retrocopy	retro_cjac_1865,
Gorilla gorilla	ENSGGOG00000026492	1 retrocopy	retro_ggor_2170,
Procavia capensis	ENSPCAG00000002433	1 retrocopy	retro_pcap_239 ,