RetrogeneDB ID: retro_mmul_57

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:117741360..117741945(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030886
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MRPL40
• Ensembl ID: ENSMMUG00000016081
• Aliases: None
• Description: 39S ribosomal protein L40, mitochondrial [Source:RefSeq peptide;Acc:NP_001253344]

Sequence

>retro_mmul_57
CTGCGCCCGATGAGTGGGCTTCTGGGAACTTGGCAGACGCAGATTAGAAATACTCACCAGCGAGCATCATTGTTGTCTTT
CTGGGAACTCATTCCCATGAGATCAGAACCTCTTCGAAAGAAGAAGAAGGTAGATCCTAAAAAAGACCAAGCAGCAAAGG
AGCGCTTGAAAAGAAGGATCCGAAAACTGGAAAAGGCTAGTCAAGAGCTAATTCCTATTGAAGATTTTATTACCCCTCTA
AAGTTCTCGAATAAAGCAAGACAGCGGCCTCAGGTGGAGCCCCCCTTTGAGGAGACTGAGAGGAGAGCTCTGCTTCTGAA
GAAGTGGTCCTTGTGCAAGCAGCAAGAGCGTAAGATGGAGAGGGACACCATCAGCGCCATGCTCGAAGCCCAGCGGGAAG
CTCTGGAGGAACTGCGACTCGAGTCCCCGAAGCTCCATGCTGAGGCCATCAAGCGGGATCCCAACCTGTTCCCCTTTGAG
AGGGAAGGGCCATGTTACACACCACCGATCCCTAACTACCAGCCCCCCGAAGGCAAGTACAGTGACGTCACCAAGGTGTA
CACACAAGTGGAGTTTAAGAGATAG

Alignment

ORF - retro_mmul_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.33 %
• Parental protein coverage: 94.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRPTSGLLGTWQRQIRNTHQRASLLSFWELIPMRSEPLRKKKKVDPKKDQAAKERLKRRIRKLEKASQEL
          LRP.SGLLGTWQ.QIRNTHQRASLLSFWELIPMRSEPLRKKKKVDPKKDQAAKERLKRRIRKLEKASQEL
Retrocopy LRPMSGLLGTWQTQIRNTHQRASLLSFWELIPMRSEPLRKKKKVDPKKDQAAKERLKRRIRKLEKASQEL

Parental  IPIEDFITPLKFLDKARQRPQVELTFEETERRALLLKKWSLYKQQEHKMERDTIRAMLEAQQEALEELRL
          IPIEDFITPLKF..KARQRPQVE..FEETERRALLLKKWSL.KQQE.KMERDTI.AMLEAQ.EALEELRL
Retrocopy IPIEDFITPLKFSNKARQRPQVEPPFEETERRALLLKKWSLCKQQERKMERDTISAMLEAQREALEELRL

Parental  ESPKLHAEAIKRDPNLFPFEREGPCYTPPIPNYQPPEGKYSDVTKVYTQVEFKK
          ESPKLHAEAIKRDPNLFPFEREGPCYTPPIPNYQPPEGKYSDVTKVYTQVEFK.
Retrocopy ESPKLHAEAIKRDPNLFPFEREGPCYTPPIPNYQPPEGKYSDVTKVYTQVEFKR

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	0.16 RPM	26.34 RPM
SRP007412_cerebellum	0.00 RPM	13.11 RPM
SRP007412_heart	0.12 RPM	17.78 RPM
SRP007412_kidney	0.12 RPM	22.89 RPM
SRP007412_liver	0.00 RPM	21.34 RPM
SRP007412_testis	0.00 RPM	16.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_57 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_57 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_57 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001053	1 retrocopy	retro_acar_149,
Ailuropoda melanoleuca	ENSAMEG00000011421	1 retrocopy	retro_amel_257,
Callithrix jacchus	ENSCJAG00000001584	1 retrocopy	retro_cjac_3220,
Equus caballus	ENSECAG00000009876	1 retrocopy	retro_ecab_687,
Homo sapiens	ENSG00000185608	1 retrocopy	retro_hsap_1020,
Gorilla gorilla	ENSGGOG00000012336	1 retrocopy	retro_ggor_807,
Myotis lucifugus	ENSMLUG00000002456	1 retrocopy	retro_mluc_1950,
Macaca mulatta	ENSMMUG00000016081	1 retrocopy	retro_mmul_57 ,
Mustela putorius furo	ENSMPUG00000003865	1 retrocopy	retro_mputfur_394,
Nomascus leucogenys	ENSNLEG00000005372	1 retrocopy	retro_nleu_899,
Pongo abelii	ENSPPYG00000011578	1 retrocopy	retro_pabe_857,
Rattus norvegicus	ENSRNOG00000049686	1 retrocopy	retro_rnor_1624,
Tarsius syrichta	ENSTSYG00000014747	1 retrocopy	retro_tsyr_1589,