RetrogeneDB ID: retro_ptro_774

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:78069273..78069942(-)
• Located in intron of: ENSPTRG00000005247

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM213A
• Ensembl ID: ENSPTRG00000002685
• Aliases: None
• Description: family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]

Sequence

>retro_ptro_774
CTTGAGGACCCAAGGTGCTTCTCTGTGTGGATGCGGTCCATGGGTGCAGGAGCCCTTGGAGGCTGCTGCCTTGGCACTGA
TGCTGGCCAACACAGATGTATTTTTGTCCAAGCCCTGGAAAGAGGTGCTGGAGTACCTGGAGAATATAGACCTGAAAACA
CTGGAGAAGTAACCAATGAGTTTCAAAGCAAAGGAGCTATCGGGAGAAGAATGGAGTTGTGATTGTGGCTGTGCCAGGCT
GTTTTCTCTGGCAAGAGGGGTTGCAGATCTGTCCTCCCTGCAACCCAAGTTGGATAAGCTGGGCATCTCCCTCTATGCAG
TCATTAAAGAGCAGGTCAGGACTGACATAAAGTTTTTCCAGCCTTGTTTCAAAAGAGAAATCTTCCTGGATGATAATAAA
AAGTTCTATGATCTACAAAGACAGAAGATGATATTTATGGGATTTAGCCCTCTGGGAGTGTGGTACAACTACCTCCAGCC
AGGAATCGAGGCTTCCCTGGAAGCCTGGAAAGCCAAGGCTTCATCCTCAGGGGAGTTTTTGTGGTGGGATCAGGAAAGCA
GGGGATTCCCGAGCATGGAGAAAAAGAATATGGAGACAAAGTAAACTCACTTTCTGTTCTGGAAGCTGCTAGGAAGATCA
AACCAGAGACTTTGGCCTCAGAGAAAAAA

Alignment

ORF - retro_ptro_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LQDPSFFTMGMWSIGAGALG-AAALALLLANTDVFLSKPQKAALEYLEDIDLKTLEKEPRTFKAKELW-E
          L.DP..F...M.S.GAGALG.AAALAL.LANTDVFLSKP.K..LEYLE.IDLKTLEK.P..FKAKEL..E
Retrocopy LEDPRCFSVWMRSMGAGALG>AAALALMLANTDVFLSKPWKEVLEYLENIDLKTLEK*PMSFKAKELS>E

Parental  KNGAVIMAVRRPGCFLCREE-AADLSSLKSTLDQLGVPLYAVVKEHIRTEVKDFQPYFKGEIFLDEKKKF
          KNG.VI.AV..PGCFL..E...ADLSSL...LD.LG..LYAV.KE..RT..K.FQP.FK.EIFLD..KKF
Retrocopy KNGVVIVAV--PGCFLWQEG<VADLSSLQPKLDKLGISLYAVIKEQVRTDIKFFQPCFKREIFLDDNKKF

Parental  YGPQRRKMMFMGFIRLGVWYNFFR-AWNGGFSGNLEGEGFILGGVFVVGSGKQGILLEHREKEFGDKVNL
          Y..QR.KM.FMGF..LGVWYN....A.N.GF.G.LE..GFIL.GVFVVGSGKQGI..EH.EKE.GDKVN.
Retrocopy YDLQRQKMIFMGFSPLGVWYNYLQ<ARNRGFPGSLESQGFILRGVFVVGSGKQGI-PEHGEKEYGDKVNS

Parental  LSVLEAAKMIKPQTLASEKK
          LSVLEAA..IKP.TLASEKK
Retrocopy LSVLEAARKIKPETLASEKK

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	83.17 RPM
SRP007412_cerebellum	0.00 RPM	36.64 RPM
SRP007412_heart	0.00 RPM	39.67 RPM
SRP007412_kidney	0.00 RPM	76.34 RPM
SRP007412_liver	0.00 RPM	111.59 RPM
SRP007412_testis	0.00 RPM	33.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_774 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_774 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1135
Gorilla gorilla	retro_ggor_886
Pongo abelii	retro_pabe_944
Macaca mulatta	retro_mmul_881
Callithrix jacchus	retro_cjac_3312

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000813	1 retrocopy	retro_chof_878,
Callithrix jacchus	ENSCJAG00000003657	1 retrocopy	retro_cjac_3312,
Dasypus novemcinctus	ENSDNOG00000001981	3 retrocopies	retro_dnov_1843, retro_dnov_1901, retro_dnov_868,
Homo sapiens	ENSG00000122378	2 retrocopies	retro_hsap_1135, retro_hsap_4076,
Gorilla gorilla	ENSGGOG00000013246	2 retrocopies	retro_ggor_2733, retro_ggor_886,
Microcebus murinus	ENSMICG00000007485	2 retrocopies	retro_mmur_1346, retro_mmur_1481,
Macaca mulatta	ENSMMUG00000021773	3 retrocopies	retro_mmul_2351, retro_mmul_2409, retro_mmul_881,
Mus musculus	ENSMUSG00000021792	1 retrocopy	retro_mmus_2227,
Otolemur garnettii	ENSOGAG00000013638	7 retrocopies	retro_ogar_2126, retro_ogar_2435, retro_ogar_2562, retro_ogar_3327, retro_ogar_420, retro_ogar_580, retro_ogar_784,
Procavia capensis	ENSPCAG00000009696	1 retrocopy	retro_pcap_281,
Pongo abelii	ENSPPYG00000025862	4 retrocopies	retro_pabe_3345, retro_pabe_643, retro_pabe_738, retro_pabe_944,
Pan troglodytes	ENSPTRG00000002685	2 retrocopies	retro_ptro_2763, retro_ptro_774 ,
Rattus norvegicus	ENSRNOG00000011140	1 retrocopy	retro_rnor_1517,