RetrogeneDB ID: retro_ggor_1710

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:10563941..10564522(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSGGOG00000015747
• Aliases: None
• Description: None

Sequence

>retro_ggor_1710
ACAGGTGTCAGTGTGGAGGCATTTGATCTAATGTTCCAAGCTAAAACAGTGAATATATTGAATCAGATAGGAAAGCCTGA
GATGGTTACTGGTTGGCATCACAGTCACTTGGCTTGGTTGCTGGGGTTTCTGGGGTGGATATCAGTACTCAGCCGTGTTT
TGAAGGCTTGTCAGAGGGAGCTTTGACGGTGGTTGTGGATTCCATTCGGAGTGTAAAAGGGAAGGTTGTTAGTGATGCCT
TCAGGTTAATCAATGCTAATATGATGGTCTTGGTACATGAACCAAGACTAACAACTTCAAATATGAGTCACTTAAACAAG
CCATCTATCCAGGCATTAATTGATGGATGAAACATACATTATTACTCTATTACTGTTAACTATCAGAAAAATAAGCTGGA
ATAGAAGATGTTGCTAAATTTGCATCAGAAGAGTTGAATGGAAGGTTTGACACTTCGGGATTACAATGAACATTGTAAAT
ACAATGATTTAGTATTAAAATAAATGCTGGAATTGGCCAAGAATTACAAAAAGGCTGTAGATGAAGAAGATGAGATGACA
CCTAAACAGCTGGCAATAGAG

Alignment

ORF - retro_ggor_1710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.31 %
• Parental protein coverage: 62.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSH-PGFGCWLSGVDINTQQSFEALSERAVAVVVDPI
          TGVSVEA.D..FQAK....L.Q.G.PEMV.GW.HSH..G.....SGVDI.TQ..FE.LSE.A..VVVD.I
Retrocopy TGVSVEAFDLMFQAKTVNILNQIGKPEMVTGWHHSH<LGLVAGVSGVDISTQPCFEGLSEGALTVVVDSI

Parental  QSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLL
          .SVKGKVV.DAFRLINANMMVL.HEPR.TTSN..HLNKPSIQALI.G.N.HYYSIT.NY.KN.LE.KMLL
Retrocopy RSVKGKVVSDAFRLINANMMVLVHEPRLTTSNMSHLNKPSIQALIDG*NIHYYSITVNYQKNKLE*KMLL

Parental  NLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNYNKAVEEEDKMTPEQLAIK
          NLH.KS.MEGLTL.DY.EHCK.N..V.K.MLELAKNY.KAV.EED.MTP.QLAI.
Retrocopy NLHQKS*MEGLTLRDYNEHCKYNDLVLK*MLELAKNYKKAVDEEDEMTPKQLAIE

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	35.34 RPM
SRP007412_cerebellum	0.00 RPM	24.43 RPM
SRP007412_heart	0.00 RPM	5.91 RPM
SRP007412_kidney	0.00 RPM	37.58 RPM
SRP007412_liver	0.00 RPM	22.16 RPM
SRP007412_testis	0.00 RPM	58.33 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_1710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1710 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1636
Pongo abelii	retro_pabe_2100

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710 ,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955, retro_ogar_3213,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,