RetrogeneDB ID: retro_mmul_2178

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:118322331..118322993(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000029343
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSMMUG00000008084
• Aliases: None
• Description: charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]

Sequence

>retro_mmul_2178
GTGTTTCGGACACTGTTCGGGACTGGAGGCGGGTAAGGCCGGCAAGGGCGGCCCGATCCCCCAGGAGGCCATCCAGCGGC
TGCAGGACACGGAGGAGATGTTAAGCAAGAAACAGGAATTCCTGGAGAAGAAAATCGAGCAGGAGCTGACTGCCGCCAAG
AAGCAGGGCACCAAAAACAAGCGCGCGGCCCTCCAGGCATTGAAGCGTAAGAAGAGGTATGAGAAGCGGCTGGCGCAGAT
CGACGGCACATTATCAACCATCGAGTTCCAGCGGCAGGCCCTGGAGAATGCCAACACCAACAACGAGGTGCTCAAGAACG
TGGGCTGTGCCGCCAAGGCCATGAAGGCGGCACATGACGACATGGACATCGATAAAGTTGATGAGTTAACGCAGGACATT
GCTGACCAGCAAGAACTTGCGGAGGAGATTTCAACAGCAATTTGGAAACCTGTAGGGTTTGGAGAGAAGTTTGACGAGGA
TGAGCTCATGGTGGAATTAAGAACTAGAACAGGAGGAACTAGACAAAAATTTGCTGGAAATCAGTGGACCCAAAACAGTC
CCTCTACCAAGTGTTCCCTCTATAGCCCTACCATCAAAACCCGCCAAGAAGAAAGAAGAGGAAGACAACGACATGAAGGA
TTTGGAGAAGTGGGCTGGGTCC

Alignment

ORF - retro_mmul_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87. %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFGKLFGAGGG-KAGKGGPTPQEAIQRLRDTEEMLSKKQEYLEKKIEQELTAAKKHGTKNKRAALQALKR
          VF..LFG.GGG.KAGKGGP.PQEAIQRL.DTEEMLSKKQE.LEKKIEQELTAAKK.GTKNKRAALQALKR
Retrocopy VFRTLFGTGGG>KAGKGGPIPQEAIQRLQDTEEMLSKKQEFLEKKIEQELTAAKKQGTKNKRAALQALKR

Parental  KKRYEKQLAQIDGTLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQEL
          KKRYEK.LAQIDGTLSTIEFQR.ALENANTN.EVLKN.G.AAKAMKAAHD.MDIDKVDEL.QDIADQQEL
Retrocopy KKRYEKRLAQIDGTLSTIEFQRQALENANTNNEVLKNVGCAAKAMKAAHDDMDIDKVDELTQDIADQQEL

Parental  AEEISTAISKPVGFGEEFDEDELMAEL-EELEQEELDKNLLEISGPETVPLPNVPSIALPSKPAKKKEEE
          AEEISTAI.KPVGFGE.FDEDELM.EL.E....E.LDKNLLEISGP.TVPLP.VPSIALPSKPAKKKEEE
Retrocopy AEEISTAIWKPVGFGEKFDEDELMVEL>ELEQEE-LDKNLLEISGPKTVPLPSVPSIALPSKPAKKKEEE

Parental  DDDMKELENWAGS
          D.DMK.LE.WAGS
Retrocopy DNDMKDLEKWAGS

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	0.11 RPM	115.75 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	149.54 RPM
SRP007412_cerebellum	0.26 RPM	74.71 RPM
SRP007412_heart	0.18 RPM	68.19 RPM
SRP007412_kidney	0.59 RPM	71.71 RPM
SRP007412_liver	0.28 RPM	46.59 RPM
SRP007412_testis	2.49 RPM	76.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2178 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2178 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_29

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009038	1 retrocopy	retro_amel_1612,
Canis familiaris	ENSCAFG00000007478	1 retrocopy	retro_cfam_1304,
Choloepus hoffmanni	ENSCHOG00000007288	1 retrocopy	retro_chof_2518,
Equus caballus	ENSECAG00000008311	1 retrocopy	retro_ecab_496,
Felis catus	ENSFCAG00000025893	1 retrocopy	retro_fcat_1835,
Homo sapiens	ENSG00000101421	1 retrocopy	retro_hsap_1339,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178 ,
Macaca mulatta	ENSMMUG00000012476	2 retrocopies	retro_mmul_1035, retro_mmul_1694,
Mustela putorius furo	ENSMPUG00000017821	2 retrocopies	retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys	ENSNLEG00000010020	1 retrocopy	retro_nleu_1822,
Pongo abelii	ENSPPYG00000010931	1 retrocopy	retro_pabe_1111,
Pan troglodytes	ENSPTRG00000013408	1 retrocopy	retro_ptro_915,
Pteropus vampyrus	ENSPVAG00000010293	1 retrocopy	retro_pvam_973,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,
Tarsius syrichta	ENSTSYG00000013212	1 retrocopy	retro_tsyr_1453,