RetrogeneDB ID: retro_mmul_1154

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:69757195..69758152(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003812
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COQ9
• Ensembl ID: ENSMMUG00000020473
• Aliases: None
• Description: None

Sequence

>retro_mmul_1154
ATGGCGGCGGCGGCGGCCGTGTCTGGTGCGCTTGGCCGGGCCGGCTGGAAGCTCCTGCAGTTGCGGTGCCTGCCTGTGAC
CCGTTGCCGACCAGCCCTGGTGCCACATGCCTTCCATGCTTCAGCTGTGGGGCTAAGGTCTTCCGATGAGCAGAAGCAGC
AGCCTCCCCCTTCATTTTCTCAGCAGCGTTCTGAGACACAGGGGGCAGGAAAACCTGATCCAGAGTCTTCTCATCCACCC
CCCAGGTATACAGACCAGGGCGGCGAGGAGGAGGAAGGCTATGAAAGTGAGGAGCAGCTGCAGGACCGCATCCTGACGGC
AGCCCTGGAGTTCGTGCCCACCCACGGGTGGACAGCAGAGGCGATTGCAGAAGGAGCCCAGTCTCTAGGTCTGTCCAGTG
CAGCAGCCAGCGTGTTTGGGAGGGATGGCAGTGAACTAATACTGCATTTTGTGACCGAGTGCAATGCCCGGCTCACACGC
GTGCTGGAAGAGGAGCAGAAGCTGGTACAGTTGGGCCAGGCCGAGAAGAAGAAGACAGACCAGTTCCTGAGGGATGCAGT
GGAAACCAGACTGAGAATGCTGATCCCATACATTGAGCACCGGCCCCAGGCCCTCAGCGTCCTCATGCTCCCTCACAACA
TCCCATCCAGCCTGAGCCTGCTCACCAGCATGGCGGATGACATGTGGCATTACGCTGGGGACCAGTCCACTGATTTTAAC
TGGTACACCCGCCGAGCCATGCTGGCTGGCATCTACAACACGACAGAGCTGGTGATGATGCAGGACTCCTCTCCAGACTT
TGAGGACACTTGGCGCTTCCTGGAAAACCGGATTAATGATGCAATGAACATGGGCCACACTGCCAAGCAGGTAAAGTCCA
CAGGAGAGGCACTGGTGCAAGGACTCATGGGTGCAGCGGTGACGCTCAAGAACTTGACAGGTCTAAACCAGCGTCGG

Alignment

ORF - retro_mmul_1154 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATAAAVAGALGRAGWKLLQLRCLPVTRCRPALVPRAFHASAVGLRSSDEQKQQPHPSFSQQHSETQGAE
          MA.AAAV.GALGRAGWKLLQLRCLPVTRCRPALVP.AFHASAVGLRSSDEQKQQP.PSFSQQ.SETQGA.
Retrocopy MAAAAAVSGALGRAGWKLLQLRCLPVTRCRPALVPHAFHASAVGLRSSDEQKQQPPPSFSQQRSETQGAG

Parental  KPDPESSYPPPRYTDQGGEEEEGYESEEQLQDRILTAALEFVPTHGWTAEAIAEGAQSLGLSSAAASMFG
          KPDPESS.PPPRYTDQGGEEEEGYESEEQLQDRILTAALEFVPTHGWTAEAIAEGAQSLGLSSAAAS.FG
Retrocopy KPDPESSHPPPRYTDQGGEEEEGYESEEQLQDRILTAALEFVPTHGWTAEAIAEGAQSLGLSSAAASVFG

Parental  KDGSELILHFVTECNARLTRMLEEEQKLVQLGQAEKKKTDQFLRDAVETRLRMLIPYIEHWPRALSVLML
          .DGSELILHFVTECNARLTR.LEEEQKLVQLGQAEKKKTDQFLRDAVETRLRMLIPYIEH.P.ALSVLML
Retrocopy RDGSELILHFVTECNARLTRVLEEEQKLVQLGQAEKKKTDQFLRDAVETRLRMLIPYIEHRPQALSVLML

Parental  PHNIPSSLSLLTSMVDDMWHYAGDQSTDFNWYTRRAMLAGIYNTTELVMMQDSSPDFEDTWRFLENRIND
          PHNIPSSLSLLTSM.DDMWHYAGDQSTDFNWYTRRAMLAGIYNTTELVMMQDSSPDFEDTWRFLENRIND
Retrocopy PHNIPSSLSLLTSMADDMWHYAGDQSTDFNWYTRRAMLAGIYNTTELVMMQDSSPDFEDTWRFLENRIND

Parental  AMNMGHTAKQVKSTGEALVQGLMGAAVTLKNLTGLNQRR
          AMNMGHTAKQVKSTGEALVQGLMGAAVTLKNLTGLNQRR
Retrocopy AMNMGHTAKQVKSTGEALVQGLMGAAVTLKNLTGLNQRR

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	28.80 RPM
SRP007412_brain_prefrontal_cortex	0.79 RPM	48.71 RPM
SRP007412_cerebellum	0.13 RPM	32.03 RPM
SRP007412_heart	1.18 RPM	177.07 RPM
SRP007412_kidney	0.47 RPM	66.55 RPM
SRP007412_liver	0.32 RPM	38.52 RPM
SRP007412_testis	0.49 RPM	40.48 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1154 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014726	2 retrocopies	retro_meug_1728, retro_meug_495,
Macaca mulatta	ENSMMUG00000020473	1 retrocopy	retro_mmul_1154 ,
Monodelphis domestica	ENSMODG00000013530	1 retrocopy	retro_mdom_452,