RetrogeneDB ID: retro_mmul_18

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:117129627..117130323(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000021893
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PAFAH1B3
• Ensembl ID: ENSMMUG00000012172
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa) [Source:RefSeq peptide;Acc:NP_001244209]

Sequence

>retro_mmul_18
ATGAGCCGAGAGGAGAACCCAGCCAGCAAGCCCACGCCGGTGCAGGACGTACAGGGCGACGGGCGCTGGATGTCCCTGCA
CCATCGGTTCGTGGCTGACAGCAAAGATAAAGAACCCGAAGTCGTCTTCATCGGGGACTCCTTGGTCCAGCTAATGCACC
AGTGCGAGATCTGGCGGGAGCTCTTTTCTCCTCTGCATGCACTTAACTTTGGCATCGGTGGTGATGGCACACAGCATGTA
CTGTGGCGGCTGGAGAATGGGGAGCTGGAACACATCCGGCCCAAGATTGTGGTGGTCTGGGTGGGCACCAACAACCACGG
ACACACAGCAGAGCAGGTGACTGGTGGCATCAAGGCCATTGTGCAACTGGTGAATGAGCGGCAGCCCCAGGCCCGGGTTG
TGGTGCTGGGTCTGCTTCCGCGAGGCCAGCATCCCAACCCACTTGGGGAGAAGAACCGACGGGTGAATGAGCTGGTACGG
GCAGCACTGGCTGGCCATCCTCGGGCCCACTTCCTAGATGCCGACCCTGGCTTTGTGCACTCAGATGGCACCATCAGCCA
CCATGACATGTATGATTACCTACATCTGAGCCGCCTGGGCTACACACCTGTTTGCCGGGCTCTGCACTCCCTGCTTCTGC
GTCTGCTGGCCCAAGACCAAGGCCAAGGTGCTCCCCTGCTGGAGCCCGCACCCTAA

Alignment

ORF - retro_mmul_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSREENPASKPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQCEIWRELFSPLHALNF
          MSREENPASKPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQCEIWRELFSPLHALNF
Retrocopy MSREENPASKPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQCEIWRELFSPLHALNF

Parental  GIGGDGTQHVLWRLENGELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLP
          GIGGDGTQHVLWRLENGELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLP
Retrocopy GIGGDGTQHVLWRLENGELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLP

Parental  RGQHPNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHS
          RGQHPNPL.EKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHS
Retrocopy RGQHPNPLGEKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHS

Parental  LLLRLLAQDQGQGAPLLEPAP
          LLLRLLAQDQGQGAPLLEPAP
Retrocopy LLLRLLAQDQGQGAPLLEPAP

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	3.92 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	23.01 RPM
SRP007412_cerebellum	0.00 RPM	3.87 RPM
SRP007412_heart	0.00 RPM	0.82 RPM
SRP007412_kidney	0.00 RPM	2.23 RPM
SRP007412_liver	0.00 RPM	2.06 RPM
SRP007412_testis	0.00 RPM	2.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_18 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_18 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019787	1 retrocopy	retro_btau_547,
Canis familiaris	ENSCAFG00000004847	1 retrocopy	retro_cfam_610,
Dasypus novemcinctus	ENSDNOG00000002870	1 retrocopy	retro_dnov_1276,
Macaca mulatta	ENSMMUG00000002050	2 retrocopies	retro_mmul_2481, retro_mmul_892,
Macaca mulatta	ENSMMUG00000012172	1 retrocopy	retro_mmul_18 ,
Mustela putorius furo	ENSMPUG00000007574	1 retrocopy	retro_mputfur_351,
Rattus norvegicus	ENSRNOG00000020481	1 retrocopy	retro_rnor_976,