RetrogeneDB ID: retro_mmul_1691

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:81428986..81429285(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4648
• Ensembl ID: ENSMMUG00000001913
• Aliases: None
• Description: 28S ribosomal protein S23, mitochondrial [Source:RefSeq peptide;Acc:NP_001253417]

Sequence

>retro_mmul_1691
ATTGGAGCAAAATTCTATTCAGCCTACAAATCTGGTCAAAAGTTTTTGATCTGTTTAATCCAAGCTTCAAGTCTACCTGT
CAATGCTTTGTGAAGTATATTGAGCTGCAGAAACTTAAAGAAACAGATGAAGAGAAGTTATTTGTAGAAATAGGGAAGGC
TTTATTGGCAGAAAGTGTAATTTTAAGATGAGTCAGAGAAGCAAGGACTCAACAGGAAGGTAGTCACGTTTCCTGGACAT
CTGAACACATGATTTTCAGACCCCAAACTGCATTGAAAGAAAACCAGCCTCAGAAGGAA

Alignment

ORF - retro_mmul_1691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.51 %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRAKFYSVYGSGQR-AFDLFNPNYKSTCQRFVEKYTELQKLGETDEEKLFVETGKALLAEGVILRRVGEA
          I.AKFYS.Y.SGQ...FDLFNP..KSTCQ.FV.KY.ELQKL.ETDEEKLFVE.GKALLAE.VILR.V.EA
Retrocopy IGAKFYSAYKSGQK<VFDLFNPSFKSTCQCFV-KYIELQKLKETDEEKLFVEIGKALLAESVILR*VREA

Parental  RTQHEGSHDSWKSEHLSVRPQTAVEENETQKE
          RTQ.EGSH.SW.SEH...RPQTA..EN..QKE
Retrocopy RTQQEGSHVSWTSEHMIFRPQTALKENQPQKE

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	17.26 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.88 RPM
SRP007412_cerebellum	0.00 RPM	14.79 RPM
SRP007412_heart	0.06 RPM	30.21 RPM
SRP007412_kidney	0.00 RPM	17.96 RPM
SRP007412_liver	0.00 RPM	8.15 RPM
SRP007412_testis	0.00 RPM	13.65 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1691 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1691 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3727
Pan troglodytes	retro_ptro_2523
Pongo abelii	retro_pabe_3131

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014008	1 retrocopy	retro_cjac_3047,
Cavia porcellus	ENSCPOG00000008761	1 retrocopy	retro_cpor_1175,
Felis catus	ENSFCAG00000005711	1 retrocopy	retro_fcat_963,
Homo sapiens	ENSG00000181610	1 retrocopy	retro_hsap_3727,
Macaca mulatta	ENSMMUG00000001913	1 retrocopy	retro_mmul_1691 ,
Mustela putorius furo	ENSMPUG00000015372	1 retrocopy	retro_mputfur_1274,
Nomascus leucogenys	ENSNLEG00000008072	1 retrocopy	retro_nleu_1972,
Pongo abelii	ENSPPYG00000025941	1 retrocopy	retro_pabe_3131,
Pan troglodytes	ENSPTRG00000009440	1 retrocopy	retro_ptro_2523,
Tarsius syrichta	ENSTSYG00000009862	1 retrocopy	retro_tsyr_2077,