RetrogeneDB ID: retro_mmul_1880

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:55588372..55588798(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90B
• Ensembl ID: ENSMMUG00000020154
• Aliases: None
• Description: coiled-coil domain-containing protein 90B, mitochondrial [Source:RefSeq peptide;Acc:NP_001247740]

Sequence

>retro_mmul_1880
CAAGAGCCAATGGCTCATTTGGGCTCTATCAGGAAAGAAATGGGCATCCTAGAGAAAAGTGAATTCACAAATCTGAGAGC
AGAGAATGAGAAAATGAAAACTGAATTAGACCAAGTTAAGCAACAATCAATACATGAAACCAGTTGAATCAGAGCAGATA
ATAAAATGGATATCAACCTAGAAAGGAGCGGAGTTACAGACATGTTTACAGATTAAGAAAAGCAACTTAAGGAAGCAACT
ACAGAATTTACAAAAACGGATCCCCAAACCAAAAGTATTATTTCAGTGACCAGTAATAAAACTGATGCAGAAATTGCTTC
CTTAAAAACACTGATGGAGTCTAACAAACTTGAGACAGTTCCTTATCTTGCAGTCTTGGTATTTAATTGCCTGGCAGTAG
CATTGGGATTTTAGAGATTCGGGAAG

Alignment

ORF - retro_mmul_1880 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.99 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQLMAHLDSIRKDMVILEKSEFANLRAENEKMKIELDQVKQQLMHETSRIRADNKLDINLERSRVTDMFT
          Q..MAHL.SIRK.M.ILEKSEF.NLRAENEKMK.ELDQVKQQ..HETS.IRADNK.DINLERS.VTDMFT
Retrocopy QEPMAHLGSIRKEMGILEKSEFTNLRAENEKMKTELDQVKQQSIHETS*IRADNKMDINLERSGVTDMFT

Parental  DQEKQLMETTTEFTKKDTQTKSIISETSNKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRF
          D.EKQL.E.TTEFTK.D.QTKSIIS.TSNK.DAEIASLKTLMESNKLET..YLA..VF.CLA.ALGF.RF
Retrocopy D*EKQLKEATTEFTKTDPQTKSIISVTSNKTDAEIASLKTLMESNKLETVPYLAVLVFNCLAVALGF*RF

Parental  WK
          .K
Retrocopy GK

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	15.91 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.42 RPM
SRP007412_cerebellum	0.00 RPM	18.02 RPM
SRP007412_heart	0.00 RPM	8.60 RPM
SRP007412_kidney	0.00 RPM	10.09 RPM
SRP007412_liver	0.00 RPM	5.34 RPM
SRP007412_testis	0.00 RPM	24.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1880 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1880 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1880 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880 , retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366,