RetrogeneDB ID: retro_pabe_2100

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:10562342..10562923(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD14
• Ensembl ID: ENSPPYG00000012881
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 [Source:HGNC Symbol;Acc:16889]

Sequence

>retro_pabe_2100
ACAGGTGTCAGTGTGGAGGCATTTGACCTAATGTTCCAAGCTAAAACGGTGTATATATTGAATCAGACAGGAAAGCTTGA
GATGGTTACTGGTTGGCATCACAGTCACTTGGCTTGGTTGCTGGGGTTTCTGGGGTGGATATCAGTACTCAACCGAGTTT
TGAAGGCTTGTCAGAGGGAGCTTTGACGGTGGTTGTGGATTCCATTCAGAATGTAAAAGGGAAGGTTGTCAGTGATGCCT
TCAGGTTGATCAATGCTAATATGATGGTCTTGGTACATGAACCGAGACTAACAACTTCAAATATGAGTCACTTAAACAAG
CCATCTATCCAGGCATTAATTGATGGATGAAACAGATATTATTACTCTATTACTGTTAACTATCAGAAAAGTAAACTGGA
ATAGAAGATGTTGCTAAATTTGCATAAGAAGAGTTGAATGGAAGGTTTGACACTTCGGGATTACAATGAACATTGTAAAT
ACAATGATTTAGTATTAAAATAGGTGCTGGAATTGGCCAAGAATTACAAAAAGGCTGTAGATGAAGAAGATGAAATGACA
CCTAAACAGCTGGCAATAGAG

Alignment

ORF - retro_pabe_2100 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.QTG..EMV.GW.HSH..G.....SGVDI.TQ.SFE.LSE.A..VVVD.I
Retrocopy TGVSVEAFDLMFQAKTVYILNQTGKLEMVTGWHHSH<LGLVAGVSGVDISTQPSFEGLSEGALTVVVDSI

Parental  QSVKGKVVIDAFRLINANMMVLGHEPRQTTSNLGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLL
          Q.VKGKVV.DAFRLINANMMVL.HEPR.TTSN..HLNKPSIQALI.G.NR.YYSIT.NY.K..LE.KMLL
Retrocopy QNVKGKVVSDAFRLINANMMVLVHEPRLTTSNMSHLNKPSIQALIDG*NRYYYSITVNYQKSKLE*KMLL

Parental  NLHKKSWMEGLTLQDYSEHCKHNESVVKEMLELAKNYNKAVEEEDKMTPEQLAIK
          NLHKKS.MEGLTL.DY.EHCK.N..V.K..LELAKNY.KAV.EED.MTP.QLAI.
Retrocopy NLHKKS*MEGLTLRDYNEHCKYNDLVLK*VLELAKNYKKAVDEEDEMTPKQLAIE

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	31.52 RPM
SRP007412_cerebellum	0.00 RPM	30.40 RPM
SRP007412_heart	0.00 RPM	15.32 RPM
SRP007412_kidney	0.00 RPM	26.29 RPM
SRP007412_liver	0.00 RPM	23.84 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2100 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2100 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1636
Gorilla gorilla	retro_ggor_1710

---

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,