RetrogeneDB ID: retro_ggor_2968

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:137763843..137764554(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16ORF72
• Ensembl ID: ENSGGOG00000010744
• Aliases: None
• Description: None

Sequence

>retro_ggor_2968
GAGCTGCAGGAGGAGGCGGCTGCAGAGTTGGCAGGGCTCAAGAGCGAGAAGCAGAAGCTGTGGCACCTCTTCCAGATCTC
GGCCACCGCCGTTGCTCAGCTTTACAAGGATTCTGGGTGCCAACAGCAAGGACTTTCCATGTGGGACCCCTTCCAGAATG
CGGCCATGGCCGTGACCAGCCTCTACAAAGAGAGCGGGGATGCCCACCAACGAAGTTTTGACTTGGGTGTCCAGGTTGGC
CACCAGCGTCGCATCAAAGATGTGCTGGAGTGGGTGAAAAAGGGCCGGAGCACCATTCGTCGCGAAGACTTGATTAGCTT
CCTGTGTGGCAAAGTGCCCCCCGCTCCTCCTCCACCTCGAACTCCTAGGACACCCCCGAAGCCACCCACTGGGGTCACCA
GCCAGGCTGTGGCAACTGAGTCCAGCTCATCGGTGGACGTCGACCTGCAGCCCTTCCAGGAGGCGATCGCCCTGCATGGC
CTCAGTGGTGCTATGGCCGGCATCAGCATGCGATCGGGCGACTCGCCTCAAGACAGCGGTGTCGCTAGCAGTGGGCGCCG
AAAAAGTAGCTTCTTGGAGGACGACTTGAATCCCTTCGACTCAGAGGAACTGGCCCTCCACCTGGACAGTGGGGGGGTCC
GCAAGCGCACCTCGGCCCAATGCAGTGATGGCATCACAGACTCCCCAATCCAAAAGCGCAACCGAATGGTC

Alignment

ORF - retro_ggor_2968 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.25 %
• Parental protein coverage: 85.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELQEEAAAA-AQPEHKQQKLWHLFQNSATAVAQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQ
          ELQEEAAA..A......QKLWHLFQ.SATAVAQLYKD..CQQ.GLS.W.PFQNAA.AVT.LYKES.D.HQ
Retrocopy ELQEEAAAELAGLKSEKQKLWHLFQISATAVAQLYKDSGCQQQGLSMWDPFQNAAMAVTSLYKESGDAHQ

Parental  RSFDIGIQIGYQRRNKDVLAWVKKRRRTIRREDLISFLCGKVPP----PRNSRAPPRLTVVSPNRATSTE
          RSFD.G.Q.G.QRR.KDVL.WVKK.R.TIRREDLISFLCGKVPP....PR..R.PP.........A..TE
Retrocopy RSFDLGVQVGHQRRIKDVLEWVKKGRSTIRREDLISFLCGKVPPAPPPPRTPRTPPKPPTGVTSQAVATE

Parental  TSSSVETDLQPFREAIALHGLSGAMASISVRSSTPGSPTHVSSGSNASRRRNGLHDVDLNTFISEEMALH
          .SSSV..DLQPF.EAIALHGLSGAMA.IS.RS...G.....S......RR.......DLN.F.SEE.ALH
Retrocopy SSSSVDVDLQPFQEAIALHGLSGAMAGISMRS---GDSPQDSGVASSGRRKSSFLEDDLNPFDSEELALH

Parental  LDNGGTRKRTSAQCGDVITDSPTHKRNRMI
          LD.GG.RKRTSAQC.D.ITDSP..KRNRM.
Retrocopy LDSGGVRKRTSAQCSDGITDSPIQKRNRMV

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	1.34 RPM	19.85 RPM
SRP007412_cerebellum	1.06 RPM	18.48 RPM
SRP007412_heart	0.00 RPM	8.22 RPM
SRP007412_kidney	0.00 RPM	31.20 RPM
SRP007412_liver	0.11 RPM	29.73 RPM
SRP007412_testis	1.14 RPM	68.27 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2968 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Pan troglodytes	retro_ptro_3172
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,