RetrogeneDB ID: retro_ptro_1636

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:124328003..124328584(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSPTRG00000012575
• Aliases: None
• Description: None

Sequence

>retro_ptro_1636
ACAGGTGTCAGTGTGGAGGCATTTCATCTAATGTTCCAAGCTAAAACGGTGAATATATTGAATCGGATAGGAAAGCCTGA
GATGGTAACTGGTTGGCATCACAGTCACTTAGCTTGGTTGCTGGGGTTTCTGGGGTGGATATCAGTACTCAGCCGAGTTT
TAAAGGCTTGTCAGAGGGAGCTTTGACGGTGGTTGTTGATTCCATTCAGAGTGTAAAAGGGAAGGTTGTTAGTGATGCCT
TCAGGTTAATCAATGCTAATATGATGGTCTTGGTACATGAACCAAGACTAACAACTTCAAATATGAATCACTTAAACAAG
CCATCTATCCAGGCATTAATTGATGGATGAAACAGACATTATTACTCTATTACTGTTAACTATCAGAAAAATAAACTGGA
ATAGAAGATGTTGCTAAATTTGCATAAGAAGAGTTGAATGGAAGGTTTGACACTTCAGGATTACAATGAACATTATAAAT
ACAATGATTTAGTATTAAAATAGATGCTGGAATTGGCCAAGAATTACAAAAAGGCTGTAGATGAAGAAGATGAGATGACA
CCTAAACAGCTGGCAATAGAG

Alignment

ORF - retro_ptro_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.79 %
• Parental protein coverage: 62.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCWLSG-VDINTQQSFEALSERAVAVVVDPI
          TGVSVEA....FQAK....L...G.PEMV.GW.HSH........G.VDI.TQ.SF..LSE.A..VVVD.I
Retrocopy TGVSVEAFHLMFQAKTVNILNRIGKPEMVTGWHHSHLAWLLGFLG<VDISTQPSFKGLSEGALTVVVDSI

Parental  QSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLL
          QSVKGKVV.DAFRLINANMMVL.HEPR.TTSN..HLNKPSIQALI.G.NRHYYSIT.NY.KN.LE.KMLL
Retrocopy QSVKGKVVSDAFRLINANMMVLVHEPRLTTSNMNHLNKPSIQALIDG*NRHYYSITVNYQKNKLE*KMLL

Parental  NLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNYNKAVEEEDKMTPEQLAIK
          NLHKKS.MEGLTLQDY.EH.K.N..V.K.MLELAKNY.KAV.EED.MTP.QLAI.
Retrocopy NLHKKS*MEGLTLQDYNEHYKYNDLVLK*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	33.09 RPM
SRP007412_cerebellum	0.00 RPM	40.29 RPM
SRP007412_heart	0.00 RPM	40.16 RPM
SRP007412_kidney	0.03 RPM	38.99 RPM
SRP007412_liver	0.00 RPM	52.83 RPM
SRP007412_testis	0.00 RPM	87.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1636 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1636 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1710
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,