RetrogeneDB ID: retro_mmul_2027

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:95205069..95205622(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSMMUG00000022552
• Aliases: None
• Description: 40S ribosomal protein S9 [Source:RefSeq peptide;Acc:NP_001252588]

Sequence

>retro_mmul_2027
CAGAAAACCTGTGTGATCACAGGGAGACCCTTTGAGAAATCCCCCCTCAACCAAGAACTAAAGCTGATAGGTAAGTGTGG
CCTCCAGAGCAAATGTGACATCTGGAGAGTCAAATTTACCCTGGACAAGTCTGCAGAGCTGCCCAGGAGCTGCTGATGTT
TGCTGAGAAGGACCCATGGCCTCTGTTTGAAGGCAGTGCCCTGCTGCAGTGACTTATTCACATCAGAGTGCAGTACAGGG
ACAGAATGAAACTAGATTGCAACCTATTCCTGAAGATTGAGGCTTTCCTGCAGAGATGCCTGCAGACCCAGTTCTTCAAG
CCAGGGTTTGGCCAAGTCCAGTCATCATGCCCCTGTGCTGATCCACTAGCACCATATCTGGGTCTGCAGGTGGTGAACAT
CCTGTCTGTACTTCACTGACTGCCTGGACTCCCAGAAGCACGGCAACTTCTCCCTTTGCTCTTTGTTTGGCAGTGGTCAC
CTGGGCCTCCTGAAGAGAATTCCAAGAAGGACCAGGGTTGGGCTGGAGAGCCCCTGGAGATAACCAAGAGGAG

Alignment

ORF - retro_mmul_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 94.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAK-IRKAARELLTLDEKDPRRLFEGNALL
          .KT.V...RPFEKS.L.QELKLIG..GL..K...WRVKFTL.K....AA.ELL...EKDP..LFEG.ALL
Retrocopy QKTCVITGRPFEKSPLNQELKLIGKCGLQSKCDIWRVKFTLDK<VCRAAQELLMFAEKDPWPLFEGSALL

Parental  RRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFK-LGLAKSIHHARVLIRQRHIRVRKQVVNIPSF
          ..L..I.V.....MKLD..L.LKIE.FL.R.LQTQ.FK..GLAKS.HHA.VLI...HI.V.........F
Retrocopy Q*LIHIRVQYRDRMKLDCNLFLKIEAFLQRCLQTQFFK>QGLAKSSHHAPVLIH*HHIWVCRW*TSCLYF

Parental  IVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAK-KGQGGAGAGDDEEE
          ...LDSQKH..FSL.S..G.G..G..KR......G.G....GD..EE
Retrocopy TDCLDSQKHGNFSLCSLFGSGHLGLLKRIPRR>PGLGWRAPGDNQEE

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	35.74 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	90.20 RPM
SRP007412_cerebellum	0.06 RPM	31.58 RPM
SRP007412_heart	0.00 RPM	121.72 RPM
SRP007412_kidney	0.00 RPM	104.93 RPM
SRP007412_liver	0.00 RPM	129.87 RPM
SRP007412_testis	0.00 RPM	79.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2027 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2027 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2190

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000022552	2 retrocopies	retro_mmul_1664, retro_mmul_2027 ,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pongo abelii	ENSPPYG00000010377	5 retrocopies	retro_pabe_1343, retro_pabe_1701, retro_pabe_1845, retro_pabe_1887, retro_pabe_2671,
Rattus norvegicus	ENSRNOG00000011355	7 retrocopies	retro_rnor_1298, retro_rnor_2577, retro_rnor_2849, retro_rnor_2902, retro_rnor_635, retro_rnor_663, retro_rnor_892,
Rattus norvegicus	ENSRNOG00000049813	3 retrocopies	retro_rnor_2082, retro_rnor_30, retro_rnor_78,