RetrogeneDB ID: retro_ptro_3172

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:140819276..140820095(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16orf72
• Ensembl ID: ENSPTRG00000007751
• Aliases: None
• Description: chromosome 16 open reading frame 72 [Source:HGNC Symbol;Acc:30103]

Sequence

>retro_ptro_3172
ATGGAGGAGCAGCAGAAGGAGGGCGAGGCCGAGGTCGCGGAGCACTGGTTTTCCAAGTGGGAGCGCCAGTGCCTGGCTGA
GGCCGAGCAGGAGGAGCAGCTGCCCCCCGAGCTGCAGGAGGAGGCGGCTGCAGAGTTGGCAGGGCTCAAGAGCGAGAAGC
AGAAGCTGTGGCACCTCTTCCAGGTCTCGGCCACCGCCGTTGCTCAGCTTTACAAGGATTCTGGGTGCCAACAGCAAGGA
CTTTCCATGTGGGACCCCTTCCAGAATGCGGCCATGGCCGTGACCAGCCTCTACAAAGAGAGTGGGGATGCCCACCAACG
AAGTTTTGACTTGGGTGTCCAGGTTGGCCACCAGCGTCGCATCAAAGATGTGCTGGAGTGGGTGAAAAAGGGCCGGAGCA
CCATTCGTCGCGAAGACTTGATTAGCTTCCTGTGTGGCAAAGTGCCCCCCGCTCCTCCTCCACCTCGCACTCCTAGGACA
CCCCCGAAGCCACCCACTGGGGTCACCAGCCAGGCTGTGGCAACTGAGTCCAGCTCATCGGTGGACGTCGACCTGCAGCC
CTTCCAGGAGGCGATCGCCCTGCATGGCCTCAGTGGTGCTATGGCCGGCATCAGCATGCGATCGGGCGACTCGCCTCAAG
ACAGCGGTGTCGCCAGCAGTGGGCGCCGAAAAAGTAGCTTCTTGGAGGACGACTTGAATCCCTTCGACTCAGAGGAACTG
GCCCTCCACCTGGACAGTGGGGGGATCCGTAAGCGCACCTCGGCCCAATGCAGTGATGGCATCACAGACTCCCCAATCCA
AAAGCGCAACCGAATGGTC

Alignment

ORF - retro_ptro_3172 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEERKEEGEAEIQEHGPEHWFSKWERQCLAEADQDEQLPP---EEAAA--AAHPEKQQKLWHLFQNSATG
          MEE...EGEAE......EHWFSKWERQCLAEA.Q.EQLPP...EEAAA..A......QKLWHLFQ.SAT.
Retrocopy MEEQQKEGEAEVA----EHWFSKWERQCLAEAEQEEQLPPELQEEAAAELAGLKSEKQKLWHLFQVSATA

Parental  VGQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIR
          V.QLYKD..CQQ.GLS.W.PFQNAA.AVT.LYKES.D.HQRSFD.G.Q.G.QRR.KDVL.WVKK.R.TIR
Retrocopy VAQLYKDSGCQQQGLSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGVQVGHQRRIKDVLEWVKKGRSTIR

Parental  REDLISFLCGKVPP----PRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISV
          REDLISFLCGKVPP....PR..R.PP.........A..TE.SSSV..DLQPF.EAIALHGLSGAMA.IS.
Retrocopy REDLISFLCGKVPPAPPPPRTPRTPPKPPTGVTSQAVATESSSSVDVDLQPFQEAIALHGLSGAMAGISM

Parental  RSSTPGSPTHVSSGSNASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
          RS...G.....S......RR.......DLN.F.SEE.ALHLD.GG.RKRTSAQC.D.ITDSP..KRNRM.
Retrocopy RS---GDSPQDSGVASSGRRKSSFLEDDLNPFDSEELALHLDSGGIRKRTSAQCSDGITDSPIQKRNRMV

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	2.41 RPM	24.51 RPM
SRP007412_cerebellum	0.68 RPM	22.55 RPM
SRP007412_heart	0.00 RPM	29.55 RPM
SRP007412_kidney	0.21 RPM	36.35 RPM
SRP007412_liver	0.33 RPM	23.99 RPM
SRP007412_testis	0.11 RPM	61.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3172 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3172 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Gorilla gorilla	retro_ggor_2968
Pongo abelii	retro_pabe_163
Mus musculus	retro_mmus_3460
Rattus norvegicus	retro_rnor_156
Sus scrofa	retro_sscr_1177
Canis familiaris	retro_cfam_147
Equus caballus	retro_ecab_1091

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172 ,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,