RetrogeneDB ID: retro_mmul_302

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:22110124..22110577(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000032498
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.9723
• Ensembl ID: ENSMMUG00000015278
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial [Source:RefSeq peptide;Acc:NP_001185668]

Sequence

>retro_mmul_302
CGTCGAGTACCTAGGAGCCGCACCTCCCGCATGGCCCCTCCGGCCAGCCGGGCACCTCAGATGAGAGCTGCACCCAGGCC
GGCACCTGTCGCTCAGCCACCAGCAGCGGCACCCCCATCTGCAGTTGGCTCTTCTGCTGCTGCACCCCGGCAGCCAGGTC
TGATGGCCCAGATGGCAACCACTGCAGCTGGCGTGGCTGTGGGCTCTGCTGTGGGACACACACTGGGTCATGCCATTACT
GGGGGCTTCAGTGGAGGAAGTAATGCTGAGCCTGCGAGTCCTGACATCACTTACCAGGAGCCACAGGGAACCCAGCTGGC
ACAGCAGCAGCAGCCTTGCTTCTATGAGATCAAACAGTTTCTGGAGTGTGCCCAGAACCAGGGTGACATCAAGCTCTGTG
AGGGTTTCAATGAGGTGCTGAAACAGTGCCGACTTGCAAACGGATTGGCCTAA

Alignment

ORF - retro_mmul_302 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.99 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGSRSRTSRMAPPASRAPQMRAAPRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVGSAV
          R..RSRTSRMAPPASRAPQMRAAPRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVGSAV
Retrocopy RVPRSRTSRMAPPASRAPQMRAAPRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVGSAV

Parental  GHTLGHAITGGFSGGSNAEPASPDITYQEPQGTQLPQQQQPCFYEIKQFLECAQNQGDIKLCEGFNEVLK
          GHTLGHAITGGFSGGSNAEPASPDITYQEPQGTQL.QQQQPCFYEIKQFLECAQNQGDIKLCEGFNEVLK
Retrocopy GHTLGHAITGGFSGGSNAEPASPDITYQEPQGTQLAQQQQPCFYEIKQFLECAQNQGDIKLCEGFNEVLK

Parental  QCRLANGLA
          QCRLANGLA
Retrocopy QCRLANGLA

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	5.83 RPM	33.05 RPM
SRP007412_brain_prefrontal_cortex	35.06 RPM	46.73 RPM
SRP007412_cerebellum	6.33 RPM	21.83 RPM
SRP007412_heart	9.13 RPM	34.92 RPM
SRP007412_kidney	6.92 RPM	24.18 RPM
SRP007412_liver	29.69 RPM	33.25 RPM
SRP007412_testis	3.69 RPM	10.40 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_302 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_302 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016050	2 retrocopies	retro_amel_500, retro_amel_976,
Bos taurus	ENSBTAG00000040295	2 retrocopies	retro_btau_397, retro_btau_768,
Canis familiaris	ENSCAFG00000010178	1 retrocopy	retro_cfam_1653,
Callithrix jacchus	ENSCJAG00000021267	1 retrocopy	retro_cjac_271,
Erinaceus europaeus	ENSEEUG00000012857	1 retrocopy	retro_eeur_398,
Echinops telfairi	ENSETEG00000008598	1 retrocopy	retro_etel_45,
Myotis lucifugus	ENSMLUG00000015151	1 retrocopy	retro_mluc_345,
Macaca mulatta	ENSMMUG00000015278	2 retrocopies	retro_mmul_160, retro_mmul_302 ,
Mus musculus	ENSMUSG00000070493	2 retrocopies	retro_mmus_2340, retro_mmus_2536,
Otolemur garnettii	ENSOGAG00000010097	5 retrocopies	retro_ogar_1161, retro_ogar_158, retro_ogar_1848, retro_ogar_2837, retro_ogar_34,
Sus scrofa	ENSSSCG00000007743	1 retrocopy	retro_sscr_515,
Ictidomys tridecemlineatus	ENSSTOG00000010512	3 retrocopies	retro_itri_1870, retro_itri_670, retro_itri_671,
Tupaia belangeri	ENSTBEG00000012905	15 retrocopies	retro_tbel_1728, retro_tbel_1891, retro_tbel_2513, retro_tbel_2593, retro_tbel_2596, retro_tbel_2658, retro_tbel_3331, retro_tbel_3764, retro_tbel_3777, retro_tbel_3954, retro_tbel_4082, retro_tbel_4368, retro_tbel_4487, retro_tbel_4728, retro_tbel_817,
Tursiops truncatus	ENSTTRG00000015185	1 retrocopy	retro_ttru_520,
Vicugna pacos	ENSVPAG00000006104	1 retrocopy	retro_vpac_48,