RetrogeneDB ID: retro_mmul_2182

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:121108727..121109207(+)
• Located in intron of: ENSMMUG00000002121

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF3
• Ensembl ID: ENSMMUG00000012624
• Aliases: None
• Description: polycomb group RING finger protein 3 [Source:RefSeq peptide;Acc:NP_001245100]

Sequence

>retro_mmul_2182
GAAAAGCCAAAGAAGTTGACCAGAAGGATTAAGCTGTGGAACACTAAGGCCCACATCACCTGCCACCTGTGTAGTGGGCA
CCTCATTGATGCAACCAGGGTGACCAAGTGTCTGCACACATTCTGTAGGGGTTGCCTGGTAAAGTATTTGCAAGAGAACA
CCACCTGCCCTGCATGTAGGACCATGATGCATCACATCCACTTACTGCAGTACATTGGTGATGATGGCACCATACATGTG
ACTGTTCACAAATTGGTATCAGGTCTCCAAGCAGCAGAAATGAAAACAGAGAGAGAATTCTGTCACAAATTGGGCATGCA
AGTGCCTGGACGGATCAAGGGGGAGACTTGTTCCACAAAACAACACTTAGATTTCCATCAGAATGGTGAAACGAAAGCAG
AAGACAGTTCAAACAAAGAGATCAAAACAGAGAAGAAGGAAAAGAACAATGATTTTCACAGAAGCGATGAGCAGGAAAGC

Alignment

ORF - retro_mmul_2182 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.62 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKPKMLTRKIKLWDINAHITCRLCSGYLIDATTVTECLHTFCRSCLVKYLEENNTCPTCRIVIHQSHPLQ
          .KPK.LTR.IKLW...AHITC.LCSG.LIDAT.VT.CLHTFCR.CLVKYL.EN.TCP.CR...H..H.LQ
Retrocopy EKPKKLTRRIKLWNTKAHITCHLCSGHLIDATRVTKCLHTFCRGCLVKYLQENTTCPACRTMMHHIHLLQ

Parental  YIGHDRTMQDIVYKLVPGLQEAEMRKQREFYHKLGMEVPGDIKGETCSAKQHLDSHRNGETKADDSSNKE
          YIG.D.T....V.KLV.GLQ.AEM...REF.HKLGM.VPG.IKGETCS.KQHLD.H.NGETKA.DSSNKE
Retrocopy YIGDDGTIHVTVHKLVSGLQAAEMKTEREFCHKLGMQVPGRIKGETCSTKQHLDFHQNGETKAEDSSNKE

Parental  AAEEKPEEDNDYHRSDEQVS
          ...EK.E..ND.HRSDEQ.S
Retrocopy IKTEKKEKNNDFHRSDEQES

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	0.00 RPM	9.19 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	17.77 RPM
SRP007412_cerebellum	0.06 RPM	6.65 RPM
SRP007412_heart	0.00 RPM	3.30 RPM
SRP007412_kidney	0.00 RPM	5.16 RPM
SRP007412_liver	0.00 RPM	2.93 RPM
SRP007412_testis	0.00 RPM	51.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2182 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707,
Macaca mulatta	ENSMMUG00000000881	1 retrocopy	retro_mmul_2591,
Macaca mulatta	ENSMMUG00000012624	1 retrocopy	retro_mmul_2182 ,
Monodelphis domestica	ENSMODG00000005677	3 retrocopies	retro_mdom_1481, retro_mdom_885, retro_mdom_985,
Nomascus leucogenys	ENSNLEG00000000926	1 retrocopy	retro_nleu_1826,
Otolemur garnettii	ENSOGAG00000015569	1 retrocopy	retro_ogar_2846,