RetrogeneDB ID: retro_mmul_14

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:42357048..42357732(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031842
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.3152
• Ensembl ID: ENSMMUG00000001671
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrial [Source:RefSeq peptide;Acc:NP_001254470]

Sequence

>retro_mmul_14
ATGGGTGGGACCACCAGCACCCGCCGGGTCACCTTCGAGGCGGACGAGAATGAGAACATCACCGTGGTGAAGGGCATCCG
GCTTTCGGAAAATGTGATTGATCGAATGAAGGAATCCTCTCCATCTGGTTCGAAGTCTCAGCGGTATTCTGGTGCTTATG
GTGCCTCAGTTTCTGATGAAGAATTGAAAAGAAGAGTAGCTGAGGAACTGGCGTTGGAGCAAGCCAAGAAAGAATCTGAA
GATCAGAAACGACTAAAGCAAGCCAAAGAGCTGGACCGAGAGAGGGCTGCTGCCAATGAGCAGTTAACCAGAGCCATCCT
TCGGGAGAGGATATCAAGCGAGGAGGAACGCGCTAAGGCAAAGCACCTGGCTAGGCAGCTGGAAGAGAAAGACCGAGTGC
TAAAGAAGCAGGATGCATTCTACAAAGAACAGCTGGCTAGACTGGAGGAGAGGAGCTCGGAGTTCTACAAAGTCACCACT
GAACAGTATCAGAAAGCTGCTGAAGAGGTGGAAGCAAAGTTCAAGCGGTATGAGTCTCATCCAGTCTGTGCTGATCTGCA
GGCCAAAATTCTTCAGTGTTACCGTGAGAACACCCACCAGACCCTCAAATGCTCCTCTCTGGCCACCCAGTATATGCACT
GTGTCAATCATGCCAAACAGAGCATGCTTGAGAAGGGAGGATAA

Alignment

ORF - retro_mmul_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MGGTTSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAEEL
          MGGTTSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAEEL
Retrocopy MGGTTSTRRVTFEADENENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAEEL

Parental  ALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQDAF
          ALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQDAF
Retrocopy ALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQDAF

Parental  YKEQLARLEERSSEFYKVTTEQYQKAAEEVEAKFKRYESHPVCADLQAKILQCYRENTHQTLKCSSLATQ
          YKEQLARLEERSSEFYKVTTEQYQKAAEEVEAKFKRYESHPVCADLQAKILQCYRENTHQTLKCSSLATQ
Retrocopy YKEQLARLEERSSEFYKVTTEQYQKAAEEVEAKFKRYESHPVCADLQAKILQCYRENTHQTLKCSSLATQ

Parental  YMHCVNHAKQSMLEKGG
          YMHCVNHAKQSMLEKGG
Retrocopy YMHCVNHAKQSMLEKGG

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	0.11 RPM	2.02 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	17.29 RPM
SRP007412_cerebellum	0.06 RPM	3.10 RPM
SRP007412_heart	0.35 RPM	19.67 RPM
SRP007412_kidney	0.00 RPM	4.11 RPM
SRP007412_liver	0.00 RPM	1.11 RPM
SRP007412_testis	0.08 RPM	5.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_14 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_14 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001312	1 retrocopy	retro_cfam_374,
Dasypus novemcinctus	ENSDNOG00000004942	1 retrocopy	retro_dnov_2559,
Homo sapiens	ENSG00000106554	3 retrocopies	retro_hsap_358, retro_hsap_3759, retro_hsap_542,
Macaca mulatta	ENSMMUG00000001671	1 retrocopy	retro_mmul_14 ,
Mus musculus	ENSMUSG00000053768	1 retrocopy	retro_mmus_3452,
Nomascus leucogenys	ENSNLEG00000012967	3 retrocopies	retro_nleu_168, retro_nleu_716, retro_nleu_904,
Oryctolagus cuniculus	ENSOCUG00000014032	1 retrocopy	retro_ocun_801,
Pongo abelii	ENSPPYG00000025827	5 retrocopies	retro_pabe_2492, retro_pabe_3161, retro_pabe_345, retro_pabe_411, retro_pabe_501,
Pan troglodytes	ENSPTRG00000019711	4 retrocopies	retro_ptro_2550, retro_ptro_282, retro_ptro_407, retro_ptro_701,
Rattus norvegicus	ENSRNOG00000013211	1 retrocopy	retro_rnor_2874,
Sorex araneus	ENSSARG00000012111	1 retrocopy	retro_sara_592,
Ictidomys tridecemlineatus	ENSSTOG00000022282	1 retrocopy	retro_itri_1301,