RetrogeneDB ID: retro_ptro_1419

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:20960297..20960815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS11
• Ensembl ID: ENSPTRG00000007420
• Aliases: None
• Description: None

Sequence

>retro_ptro_1419
AGGGTCATGGCCAGGATGCTGGTGCAGACCATCCACACAGGCACCCAGAAGATCCAAGACATTGAGGCCAAGCAGAACAT
TGAAGAGAAGATGGTAGCTCCCAGCTACACCAGCTTTAGCATTTACCCTCCCATTACAAAAGAAAAAAGCTCTCTGAGGT
GGGCAGGAAAGAAATTTGAGGAGATCCCAACTGCACACATTAGAGCATCCTACAACAACACACAGATCCAGGTAATCTCT
GCCACTAATCAGCCCCTTGCCCATTCTTCCTGTGGCACAGAGGAATTTCTGAATGCCAAGAAGGGCACAGGCATTGATGC
ACAGACAACAGGCATAGCAGCCGTGACAAAAGCTGCAGGAAAGGGTGTTACCCACATCTGAGTTGTGGTGAAAGGCCAGG
GGCCAGGACACCTGTCTGCCATCCAGGGACTGACCATGGGGGGCCTGGAAGTGATCTCAATCACAACAACACCCCCATCC
CACACAATGGCTCCTGCCCCAAGAAGGCTCCGAGGCTG

Alignment

ORF - retro_ptro_1419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 88.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVVARTPAGTICTGARQLQDAAAKQKVEQN-AAPSHTKFSIYPPIPGEESSLRWAGKKFEEIPIAHIKAS
          RV.AR....TI.TG....QD..AKQ..E....APS.T.FSIYPPI..E.SSLRWAGKKFEEIP.AHI.AS
Retrocopy RVMARMLVQTIHTGTQKIQDIEAKQNIEEKMVAPSYTSFSIYPPITKEKSSLRWAGKKFEEIPTAHIRAS

Parental  HNNTQIQVVSASNEPLAFASCGTEGFRNAKKGTGIAAQTAGIAAAARAKQKGVIHIRVVVKGLGPGRLSA
          .NNTQIQV.SA.N.PLA..SCGTE.F.NAKKGTGI.AQT.GIAA...A..KGV.HI.VVVKG.GPG.LSA
Retrocopy YNNTQIQVISATNQPLAHSSCGTEEFLNAKKGTGIDAQTTGIAAVTKAAGKGVTHI*VVVKGQGPGHLSA

Parental  MHGLIMGGLEVISIT-DNTPIPHNGCRPRKARKL
          ..GL.MGGLEVISIT..NTPIPHNG..P.KA..L
Retrocopy IQGLTMGGLEVISIT<NNTPIPHNGSCPKKAPRL

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_prefrontal_cortex	0.00 RPM	24.52 RPM
SRP007412_cerebellum	0.00 RPM	19.29 RPM
SRP007412_heart	0.00 RPM	15.42 RPM
SRP007412_kidney	0.00 RPM	30.70 RPM
SRP007412_liver	0.00 RPM	30.21 RPM
SRP007412_testis	0.00 RPM	22.45 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1419 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1419 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2458
Gorilla gorilla	retro_ggor_1531
Macaca mulatta	retro_mmul_637

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013012	2 retrocopies	retro_cjac_2601, retro_cjac_2989,
Felis catus	ENSFCAG00000014967	1 retrocopy	retro_fcat_282,
Homo sapiens	ENSG00000181991	1 retrocopy	retro_hsap_2458,
Gorilla gorilla	ENSGGOG00000015152	1 retrocopy	retro_ggor_1531,
Macaca mulatta	ENSMMUG00000013659	1 retrocopy	retro_mmul_637,
Nomascus leucogenys	ENSNLEG00000011441	1 retrocopy	retro_nleu_1902,
Ochotona princeps	ENSOPRG00000008247	1 retrocopy	retro_opri_540,
Pongo abelii	ENSPPYG00000006751	2 retrocopies	retro_pabe_1808, retro_pabe_2583,
Pan troglodytes	ENSPTRG00000007420	1 retrocopy	retro_ptro_1419 ,