RetrogeneDB ID: retro_mmul_453

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:200884592..200885434(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MMU.4154
• Ensembl ID: ENSMMUG00000008106
• Aliases: None
• Description: peroxisomal membrane protein PMP34 [Source:RefSeq peptide;Acc:NP_001244445]

Sequence

>retro_mmul_453
TTTTTTCCCCTGGATACAGCTAGACTTCGACTTCAGGTTGATGAGAAAAGAAAATCCAAAACTACACACATGGTGCTCCT
GGAGATCATTAAAGAAGAAGGACTCCTGGCACCCTATCGAGGGTGGTTTCCAGTGATTTCCAGTCTCTGCTGCTCCAATT
TTGTCTATTTCTACACTTTTAATAGCCTCAAAGCAGTCTGGGTCAAAGGTCAACGTTCTACCACTGGAAAAGATCTGGTA
GTTGAGTTTGTTGCAGGAGTAGTTAAGGTGTTACTAACAACTCCACTCTGGGTGGTAAACACCAGACTGAAGCTGCAAGG
GGCAAAATTTAGGAATGAAGACATTGTACCAACGAACTACAAAGGTATCATTGATGCTTTTCATCAGATCATTCGAGATG
AGGGAATCCCGGCTTTATGAAATGGCACATTTCCCTCATTGCTGTTGGTCTTCAATCTTGCCATCCAGTTCATGTTTTAT
GAAGGTTTAAAACAGCAGTTTTTAAAGAAACGGATGAAGCTTCTTCCTTGGATGTGTTCATCATTGGTGCAGTAGCCAAA
GCGACTGCCACCAGGCTCACCTATCCCATGCACACAGTACAGTCAATTCTGAGGTTTGGGCGTCATAGACTAAACCCAGA
AAACAGAACATTGGGAAATCTTTGGAATACTCTCTATCTTCTTCACGAACGAGTAAGGCGCTTTGGAATACTAGGACTCT
ACAAAGGCCTGGAAGCCAAACTGCTACAGACAGTCCTCACTGCTGCTCTCATGTTCCTTGTTTATGAGAAACTGACAGCT
GCCACCTTCACAGTTGTGGGGCTGAAGTGTGCACACAAACAC

Alignment

ORF - retro_mmul_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.62 %
• Parental protein coverage: 91.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFPLDTARLRLQVDEKRKSKTTHMVLLEIIKEEGLLAPYRGWFPVISSLCCSNFVYFYTFNSLKAVWVKG
          FFPLDTARLRLQVDEKRKSKTTHMVLLEIIKEEGLLAPYRGWFPVISSLCCSNFVYFYTFNSLKAVWVKG
Retrocopy FFPLDTARLRLQVDEKRKSKTTHMVLLEIIKEEGLLAPYRGWFPVISSLCCSNFVYFYTFNSLKAVWVKG

Parental  QRSTTGKDLVVGFVAGVVNVLLTTPLWVVNTRLKLQGAKFRNEDIVPTNYKGIIDAFHQIIRDEGISALW
          QRSTTGKDLVV.FVAGVV.VLLTTPLWVVNTRLKLQGAKFRNEDIVPTNYKGIIDAFHQIIRDEGI.AL.
Retrocopy QRSTTGKDLVVEFVAGVVKVLLTTPLWVVNTRLKLQGAKFRNEDIVPTNYKGIIDAFHQIIRDEGIPAL*

Parental  NGTFPSLLLVFNPAIQFMFYEGLKRQLLKKRMKL-SSLDVFIIGAVAKAIATTLTYPMQTVQSILRFGRH
          NGTFPSLLLVFN.AIQFMFYEGLK.Q.LKKRMKL.SSLDVFIIGAVAKA.AT.LTYPM.TVQSILRFGRH
Retrocopy NGTFPSLLLVFNLAIQFMFYEGLKQQFLKKRMKL<SSLDVFIIGAVAKATATRLTYPMHTVQSILRFGRH

Parental  RLNPENRTLGSLRNILYLLHQRVRRFGILGLYKGLEAKLLQTVLTAALMFLVYEKLTAATFTVMGLKRAH
          RLNPENRTLG.L.N.LYLLH.RVRRFGILGLYKGLEAKLLQTVLTAALMFLVYEKLTAATFTV.GLK.AH
Retrocopy RLNPENRTLGNLWNTLYLLHERVRRFGILGLYKGLEAKLLQTVLTAALMFLVYEKLTAATFTVVGLKCAH

Parental  TH
          .H
Retrocopy KH

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	12.10 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.33 RPM
SRP007412_cerebellum	0.00 RPM	10.78 RPM
SRP007412_heart	0.00 RPM	3.47 RPM
SRP007412_kidney	0.00 RPM	19.25 RPM
SRP007412_liver	0.00 RPM	4.00 RPM
SRP007412_testis	0.00 RPM	10.40 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_453 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_453 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004636	1 retrocopy	retro_cjac_2451,
Macaca mulatta	ENSMMUG00000008106	1 retrocopy	retro_mmul_453 ,
Monodelphis domestica	ENSMODG00000013036	1 retrocopy	retro_mdom_1808,