RetrogeneDB ID: retro_ggor_174

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 20:61073215..61073452(+)
• Located in intron of: ENSGGOG00000017041

Retrocopy information

• Ensembl ID: ENSGGOG00000027339
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DPH3
• Ensembl ID: ENSGGOG00000022108
• Aliases: None
• Description: None

Sequence

>retro_ggor_174
ATGGCAGTATTTCCTGACGAGGTGGAAATCGAGGACTTCCAATATGACGAGGACTCGGAGACATATTTCTGTCCCTGCCC
ATGCGGAGATAACTTCTCCATCACCAAGGAAGAGCTGGAGAATGGGGAAGTTGTGGCAATGTGTCCAGGCTGCTCTCTCA
TTATAAAAGTGATTTATGACAAAGATCAGTTTGCGTGTGGAGAAACAGTGCCAGTGCCTTCAGTCAACAAAGAATGA

Alignment

ORF - retro_ggor_174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 95.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETYFYPCPCGDNFSITKEDLENGEDVATCPSCSLIIKVIYDKDQFVCGETV
          MAVF.DEVEIEDFQYDEDSETYF.PCPCGDNFSITKE.LENGE.VA.CP.CSLIIKVIYDKDQF.CGETV
Retrocopy MAVFPDEVEIEDFQYDEDSETYFCPCPCGDNFSITKEELENGEVVAMCPGCSLIIKVIYDKDQFACGETV

Parental  PAPSANKE
          P.PS.NKE
Retrocopy PVPSVNKE

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	1.05 RPM	4.03 RPM
SRP007412_cerebellum	0.98 RPM	2.44 RPM
SRP007412_heart	0.22 RPM	1.34 RPM
SRP007412_kidney	1.64 RPM	8.06 RPM
SRP007412_liver	0.66 RPM	5.88 RPM
SRP007412_testis	0.93 RPM	7.77 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_174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_174 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2438
Pan troglodytes	retro_ptro_1409
Pongo abelii	retro_pabe_1795

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003916	2 retrocopies	retro_btau_797, retro_btau_967,
Canis familiaris	ENSCAFG00000005881	1 retrocopy	retro_cfam_273,
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Equus caballus	ENSECAG00000016591	1 retrocopy	retro_ecab_1095,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Felis catus	ENSFCAG00000006355	1 retrocopy	retro_fcat_656,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174 ,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Oryctolagus cuniculus	ENSOCUG00000015862	1 retrocopy	retro_ocun_1662,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,