RetrogeneDB ID: retro_ggor_1195

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:34486976..34487699(-)
• Located in intron of: ENSGGOG00000005429

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSGGOG00000008114
• Aliases: None
• Description: None

Sequence

>retro_ggor_1195
ATGCTGAGGAGCTGCGCCGGGCACCTCCGCACGCTGAGGGCCCTTTGCCAGCCACCACCAGTAGGCAGGCGCCTGCCGGG
TAGTGAGCCGCGACCCACGCTGAGGTCATTTTCTTCTGAGGAAGTCATTCTTAAGGACTATTCTGTCCCCAACCCCAGCT
GGAACAAGGACCTAAGACTGCTCTTTGACCAGTTTATGAAGAAATTTGAAGATGGCTCCTGGAAACGTTTGCCTTCATAT
AAACATACACCTACTGAAAGGATTCAAGACTTTAAAACCCATTTTCTTGACCCAAAGCTTATGAAAGAAGAACAAGTGTC
ACAGGCCCAGCTCTTCACCAGAAGCTTTGATGATGGCCTGGGCTTTGAATACATGATGTTCTACAGTGACGTTGAGAAAA
GGATGGTTTGCTTATTTCAAGGAGTCCCTTACCTAGAAGGACCACCTGGATTGATTCATGGAGGTGCCATTGCAACCATG
ATTGATGCTACTGTTGGTATGTGTGCAATGATGGCTGGGGGAATCATCATGACTGCCAATCTCAACATCAGTTGTAAAAG
ACCTATCCCTCTTTGTTCTGCTGTTATGATAAATAGCCAACTTGATAAAGTTGAAGGAAAGAAATTTTTTGTTTCCAGTA
ATGTTCAGAGTATTGATGAGAAGACCCTATACTCAGAGGCGACAAGCTTACTTATAAAGCTGAATCCTGCTAAAAGTCTG
ACA

Alignment

ORF - retro_ggor_1195 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRSCAARLRTLGVVCRPP-VGRRLPGSEPRPELRSFSSEEVILKDCSVPNPSWNKDLRLLFDQFMKKCE
          MLRSCA..LRTL...C.PP.VGRRLPGSEPRP.LRSFSSEEVILKD.SVPNPSWNKDLRLLFDQFMKK.E
Retrocopy MLRSCAGHLRTLRALCQPPPVGRRLPGSEPRPTLRSFSSEEVILKDYSVPNPSWNKDLRLLFDQFMKKFE

Parental  DGSWKRLPSYKRTPTERIQDFKTRFLDPKLMKEEQMSQAQLFTRSFDDGLGFEYVMFYNDIEKRMVCLFQ
          DGSWKRLPSYK.TPTERIQDFKT.FLDPKLMKEEQ.SQAQLFTRSFDDGLGFEY.MFY.D.EKRMVCLFQ
Retrocopy DGSWKRLPSYKHTPTERIQDFKTHFLDPKLMKEEQVSQAQLFTRSFDDGLGFEYMMFYSDVEKRMVCLFQ

Parental  GGPYLEGPPGFIHGGAIATMIDATVGMCAMMAGGIVMTANLNINYKRPIPLCSVVMINSQLDKVEGRKFF
          G.PYLEGPPG.IHGGAIATMIDATVGMCAMMAGGI.MTANLNI..KRPIPLCS.VMINSQLDKVEG.KFF
Retrocopy GVPYLEGPPGLIHGGAIATMIDATVGMCAMMAGGIIMTANLNISCKRPIPLCSAVMINSQLDKVEGKKFF

Parental  VSCNVQSVDEKTLYSEATSLFIKLNPDKSLT
          VS.NVQS.DEKTLYSEATSL.IKLNP.KSLT
Retrocopy VSSNVQSIDEKTLYSEATSLLIKLNPAKSLT

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	16.06 RPM
SRP007412_cerebellum	0.00 RPM	12.10 RPM
SRP007412_heart	0.00 RPM	6.44 RPM
SRP007412_kidney	0.00 RPM	34.43 RPM
SRP007412_liver	0.00 RPM	9.65 RPM
SRP007412_testis	0.00 RPM	37.61 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_1195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1195 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1569
Pan troglodytes	retro_ptro_1056
Pongo abelii	retro_pabe_1295

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195 , retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,