RetrogeneDB ID: retro_mmul_224

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:19489904..19490384(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030925
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.479
• Ensembl ID: ENSMMUG00000015247
• Aliases: None
• Description: succinate dehydrogenase complex, subunit D, integral membrane protein [Source:RefSeq peptide;Acc:NP_001248692]

Sequence

>retro_mmul_224
ATGGCGGTTGTCTGGAGGCTGAGTGCCCTTTGCGGTGCCCAAGGAGGCCGAGCTCTGTTGCTGCGAACCCCAGTGGTCAG
ACCTGCTCATATCTCAGCATTTCTTCAGGACCGACCTATCCCAGAATGGCGTGGAGTGCAGCACATTCACTTGTCACCCA
GGCACCATTCTGGTTCCAAGGCTGCGTCTCTCCACTGGACTAGCGAGAGGGTTGTCAGTGTTTTGCTCCTGGGTCTGCTT
CCGGCTGCTTATTTGAATCCTTGCTCTGCGATGGACTATTCCCTGGCTGCAGCCCTCACTCTTCATGGTCACTGGGGCCT
TGGACAAGTTGTTACTGACTATGTTCATGGGGATGCCTCGCAGAAAGCTGCCAAGGCAGGGCTTTTGGCACTTTCAGCTT
TAACCTTTGCTGGGCTTTGCTATTTCAACTATCACGACGTGGGCATCTGCAAAGCTGTTGCCATGCTGTGGAAGCTCTGA

Alignment

ORF - retro_mmul_224 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVVWRLSAFCGAQGGRALLLRTPVVRPAHISAFLQDRPIPEWRGVQHIHLSPRHHSGSKAASLHWTSER
          MAVVWRLSA.CGAQGGRALLLRTPVVRPAHISAFLQDRPIPEWRGVQHIHLSPRHHSGSKAASLHWTSER
Retrocopy MAVVWRLSALCGAQGGRALLLRTPVVRPAHISAFLQDRPIPEWRGVQHIHLSPRHHSGSKAASLHWTSER

Parental  VVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHDYRGLGQVVTDYVHGDASQKAAKAGLLALSALTFAGLC
          VVSVLLLGLLPAAYLNPCSAMDYSLAAALTLH...GLGQVVTDYVHGDASQKAAKAGLLALSALTFAGLC
Retrocopy VVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGLGQVVTDYVHGDASQKAAKAGLLALSALTFAGLC

Parental  YFNYHDVGICKAVAMLWKL
          YFNYHDVGICKAVAMLWKL
Retrocopy YFNYHDVGICKAVAMLWKL

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	0.56 RPM	1.01 RPM
SRP007412_brain_prefrontal_cortex	3.17 RPM	9.44 RPM
SRP007412_cerebellum	0.77 RPM	0.97 RPM
SRP007412_heart	4.30 RPM	6.89 RPM
SRP007412_kidney	5.87 RPM	6.22 RPM
SRP007412_liver	6.85 RPM	21.06 RPM
SRP007412_testis	2.26 RPM	5.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_224 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556, retro_amel_1588, retro_amel_998,
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224 ,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087, retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233, retro_pabe_2999, retro_pabe_3096,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529, retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,