RetrogeneDB ID: retro_mmul_1854

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:124486557..124487425(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10030
• Ensembl ID: ENSMMUG00000016118
• Aliases: None
• Description: dnaJ homolog subfamily C member 7 [Source:RefSeq peptide;Acc:NP_001248180]

Sequence

>retro_mmul_1854
GAAGCAGAGTCTTTGAAGCAACAAGGAAATGCACACTATGCCAAGAAAGATTACAACGAAGCTTATAACTATTAGACAAA
AGCCACAGATATGTGCCCTAAAAATGCTAGCTATTATAGTAATAGAGCAGCCATATTGATGATGCTTGGAAGGTTTTGGG
AAATGCTTGGAGATGCTTTCACAGTCAGTGAATTTGGCTGATGGTTTCTTCCGGGGACATCTACGAGAGGGCAAGTGCCA
CCTCTCTCCAGGGAATGCCATGGCAGCACATTGCAGTTTTCAGAAAGCCCTAGAACTGGATCATAACAATGCTCACTCGC
AACAGGAGTTCACAAATGCTAATGCAGTTGTGGAATAGGAGAAAGTCACAGAAACAGGTTTTGAGAAGTGGGCTTTTCAG
AAGGTTGTTTTCTGCATGGACTATGCCCTAGAATTTGCTCCTGTCTGCCATCACTTCCATATCCCTCAAAGCAGAATGTT
TAGCAATGCCGGGTCATTATCCAGAAACACAGTCTGCGGCCAGTGACATTTTATGAATGGATTCCACCAATGTGGATGCT
CTGTATGTACGCGGTCTTTGCCTTTATTATGAAGATTGTATTGAGCAGGCAGTTGTTCAGTTTTTTGTACAGGCTCTCAG
AATGGCTCCTGACCATGAGAAGGCCTGTGTTGGGTGCAGAAATGCCAGAGCATTTAACACAAAGAAAGAAGACTGGAATA
AAGCATTTAGGGAAGGAAATTACAAACTAGCTGGTGAACTGGACACGGAAGCCCTGGGATAGACCTCAACAATATAAAAG
CAATTGCTAAACTCTACTGAAACCGGGATACAGTTAATTCTGAGCTTGGGAAACTAGATGATGCAATA

Alignment

ORF - retro_mmul_1854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.42 %
• Parental protein coverage: 58.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDA-QQSVRLDDSF
          EAE..K.QGNA.YAKKDYNEAYNY.TKA.DMCPKNASYY.NRAA.LMMLGRF.E.LGDA..QSV.L.D.F
Retrocopy EAESLKQQGNAHYAKKDYNEAYNY*TKATDMCPKNASYYSNRAAILMMLGRFWEMLGDA>SQSVNLADGF

Parental  VRGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCM
          .RGHLREGKCHLS.GNAMAA..SFQ.ALELDH.NA..QQEF.NANAV.E.EK..ET.FEK..F.KVVFCM
Retrocopy FRGHLREGKCHLSPGNAMAAHCSFQKALELDHNNAHSQQEFTNANAVVE*EKVTETGFEKWAFQKVVFCM

Parental  DRALEFAPACHRFKI-LKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKA-VQFF
          D.ALEFAP.CH.F.I.LKAECLAM.G.YPE.QS.ASDIL.MDSTN.DALYVRGLCLYYEDCIE.A.VQFF
Retrocopy DYALEFAPVCHHFHI>LKAECLAMPGHYPETQSAASDIL*MDSTNVDALYVRGLCLYYEDCIEQAVVQFF

Parental  VQALRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEAL-GIDPNNIKTNAKLYCNRGT
          VQALRMAPDHEKAC..CRNA.A...KKED.NKAF.EGNYKLA.EL.TEAL.GID.NNIK..AKLY.NR.T
Retrocopy VQALRMAPDHEKACVGCRNARAFNTKKEDWNKAFREGNYKLAGELDTEAL<GIDLNNIKAIAKLY*NRDT

Parental  VNSKLRKLDDAI
          VNS.L.KLDDAI
Retrocopy VNSELGKLDDAI

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	46.28 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	57.67 RPM
SRP007412_cerebellum	0.00 RPM	35.26 RPM
SRP007412_heart	0.00 RPM	17.19 RPM
SRP007412_kidney	0.00 RPM	20.66 RPM
SRP007412_liver	0.04 RPM	4.95 RPM
SRP007412_testis	0.00 RPM	30.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1854 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1854 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1854 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3524
Pan troglodytes	retro_ptro_2393
Gorilla gorilla	retro_ggor_2382
Pongo abelii	retro_pabe_2911

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854 , retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,