RetrogeneDB ID: retro_ptro_2025

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:155967598..155968333(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000016520
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM192A
• Ensembl ID: ENSPTRG00000008148
• Aliases: None
• Description: family with sequence similarity 192, member A [Source:HGNC Symbol;Acc:29856]

Sequence

>retro_ptro_2025
TTGTTATCAAAAAGGTTAGTGTCTGAGGCAGAACTAGATGAACGGTGCAAAAGGAGGCAAGAAGAATGGGAGAAAGTTCG
AAAACCTGAAGATTCAGAAGAATGTCCAGAGGAGGTTTATGACCCTCGACCTCTATATGAAAGGCTACAGGAACAGAAGG
ACAGGAAGCAGCAGGAGTATGAGGAACAGTTCAAATTCAAAAACATGGTAAGAGGCTTAGATGAAGATGAGACCAACTTC
CTTGATGAGGTTTCTCGACAGCAGGAACTAATAGAAAAGCAACAAAGAAAAGAAGAACTGAAAGAACTGAAGGAATACAG
AAATAACCTCAAGAAGGTTGGAATTTCTCAAGAGAACAAGAAGGAAGTGGAAAAGAAACTGACTGTGAAGCCCTTAGAAA
CCAAGAACAAGTTCTCCCAGGTGAAGCTGTTGGCAGGAGCTGTGAAGCGTAAGAGCTCAGAGAGTGACAACAGTGTAAAA
AGACTGAAACCGGACCCTGAGCCAGATGACAAGAATCAAGAGCCCTCATCCTGCAAGTCTCTCAGAAACACCTCCCTGAG
TGGCCCCTCCATCCACTGCCCCTCTGCTGCAGTCTGTATCAGCATCCTCCCAGGCCTGGGCGCCTACTCTGGGAGCAGCG
ACTCTGAGTCCAGCGCAGACAGTGAAGGCACCATCAATGCCACCGGAAAGATTGTCTCCTCTATCTTCCAAACCAATACC
TTCCTTGAGGCCCCT

Alignment

ORF - retro_ptro_2025 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.65 %
• Parental protein coverage: 96.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIKKRFVSEAELDERRKRRQEEWEKVRKPEDPEECPEEVYDPRSLYERLQEQKDRKQQEYEEQFKFKNMV
          ...KR.VSEAELDER.KRRQEEWEKVRKPED.EECPEEVYDPR.LYERLQEQKDRKQQEYEEQFKFKNMV
Retrocopy LLSKRLVSEAELDERCKRRQEEWEKVRKPEDSEECPEEVYDPRPLYERLQEQKDRKQQEYEEQFKFKNMV

Parental  RGLDEDETNFLDEVSRQQELIEKQRREEELKELKEYRNNLKKVGISQENKKEVEKKLTVKPIETKNKFSQ
          RGLDEDETNFLDEVSRQQELIEKQ.R.EELKELKEYRNNLKKVGISQENKKEVEKKLTVKP.ETKNKFSQ
Retrocopy RGLDEDETNFLDEVSRQQELIEKQQRKEELKELKEYRNNLKKVGISQENKKEVEKKLTVKPLETKNKFSQ

Parental  AKLLAGAVKHKSSESGNSVKRLKPDPEPDDKNQEPSSCKSLGNTPLSGPSIHCPSAAVCIGILPGLGAYS
          .KLLAGAVK.KSSES.NSVKRLKPDPEPDDKNQEPSSCKSL.NT.LSGPSIHCPSAAVCI.ILPGLGAYS
Retrocopy VKLLAGAVKRKSSESDNSVKRLKPDPEPDDKNQEPSSCKSLRNTSLSGPSIHCPSAAVCISILPGLGAYS

Parental  GSSDSESSSDSEGTINATGKIVSSIFRTNTFLEAP
          GSSDSESS.DSEGTINATGKIVSSIF.TNTFLEAP
Retrocopy GSSDSESSADSEGTINATGKIVSSIFQTNTFLEAP

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	0.20 RPM	72.48 RPM
SRP007412_cerebellum	0.97 RPM	82.06 RPM
SRP007412_heart	0.29 RPM	33.34 RPM
SRP007412_kidney	0.21 RPM	43.10 RPM
SRP007412_liver	0.26 RPM	35.55 RPM
SRP007412_testis	1.05 RPM	145.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2025 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2025 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2025 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2994
Gorilla gorilla	retro_ggor_2074
Pongo abelii	retro_pabe_2480

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002242	1 retrocopy	retro_btau_1133,
Cavia porcellus	ENSCPOG00000001392	1 retrocopy	retro_cpor_122,
Equus caballus	ENSECAG00000009324	1 retrocopy	retro_ecab_710,
Echinops telfairi	ENSETEG00000014379	1 retrocopy	retro_etel_930,
Homo sapiens	ENSG00000172775	1 retrocopy	retro_hsap_2994,
Gorilla gorilla	ENSGGOG00000003938	1 retrocopy	retro_ggor_2074,
Macaca mulatta	ENSMMUG00000013492	1 retrocopy	retro_mmul_189,
Mus musculus	ENSMUSG00000031774	1 retrocopy	retro_mmus_428,
Nomascus leucogenys	ENSNLEG00000002716	1 retrocopy	retro_nleu_745,
Ochotona princeps	ENSOPRG00000006909	2 retrocopies	retro_opri_175, retro_opri_579,
Pongo abelii	ENSPPYG00000007382	1 retrocopy	retro_pabe_2480,
Pan troglodytes	ENSPTRG00000008148	1 retrocopy	retro_ptro_2025 ,
Tarsius syrichta	ENSTSYG00000013300	1 retrocopy	retro_tsyr_884,
Tursiops truncatus	ENSTTRG00000012791	1 retrocopy	retro_ttru_1884,
Vicugna pacos	ENSVPAG00000005973	1 retrocopy	retro_vpac_321,