RetrogeneDB ID: retro_ggor_486

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:220447220..220448710(-)
• Located in intron of: ENSGGOG00000001014

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD2
• Ensembl ID: ENSGGOG00000027136
• Aliases: None
• Description: None

Sequence

>retro_ggor_486
GCAGTGGCAGCGGAGATGGAGGAGGGAGGATGGGACAAGATGCTGGTGCAGTCCCAGCAGCCCCCAGCGGCGGTCCCCAG
CGGCATGGATGAGAAGCCAAGCGGCAAGAAGCGGCAGGATGCCGGGGACAAGGACAAAGAACAGGAGCTGTCTCAGGAAG
ATAAACAGCTTCAAGATGAACTGGAGATGCTTGTGGAATGATCGGGGAGAAGGACACATTCCTGTATCGACCAGCGCTGG
AGGAATTGCAAAGGCAGATTCGTTCTTCTACAACTTCCATGACTTTGGTGACCAAGCCTCTCAAATTTCTGCATCCACAC
TATGGCAAACTGAAGGAAATCTATGAGAACATGGCCCCTGGGAAGAATGAGCATTTTGCTGCTGACATCATCTCTGTTTT
GGCCATGACCATGAGTGGGGAGTGCGAGTGCCTCAAGTATCGGCTAGTAGGCTCCCAGAAGGAATTGGCATCATGGAGTC
ATGAGTATGTCAGGCACCTGGCAGGAGAAGTGGCTAAGGACTGGCAGGAGCTGGGTGATGCGGAGAAGGTCCAGCAGGAG
CCACTGCTCACTCTGGTGAAGGAAATCGTCCCCTACAACATGGCCCACGATGCAGAGCATGAGGCCTGCGACCTGCTTAT
GGAAATTGAGCAGTGGACATGCTGGAGAAGGACATTGATGAGAATGCATACACAAAGGTCTGCCTTTATCTCACCAGTTG
TGTGAATTACGTGTCTGAGCCTGAGAACTCAGTCCTACTGCGTTGTGCCCTGGGTGTGTTCTGAAAGTTTAGCCGCTTCC
CTAAAGCTCTGAGATTGGCATTGATGTGCAATGACATGGAGCTGGTAGAAGACATCTTCACATCCTGCAAGGACGTGGTA
GTACAGAAACAGATGGCATTCATGCTAGGCTGGCATGGGGTGTTCCTGGAGCTGAGTGAAGATGTCGAAGAGTATGAGCA
CCTGACAGAGATCATGTCCAATGTACAGCTCAACAGCGACTTCTTGGCCTTAGCTCGGGAGCTGGACATCTTGGAGCCCA
AGGTGCCTGATGACATCTACAAAACCCACCTAGAGAACAACAGGTTTGGGGGCAGTGGCTCTCAGGTGGACTCTGCCTGC
ATGAACCTGGCCTCCTCTTTTGTGAATGGCTTTGTGAATGCAGCTTTTGTTTAAGACAAGCTGCTAACAGATGATGGCAA
CAAATGGCTTTACAAGAACAAGGACCACGGAATGTTGAGTGCAGCTGCATCTGTTGGAATGCTGCTGCTGTGGGATGTGG
ATGGTGGCCTCATTCAGATTGACAAGTAACCTGTACTCCTCTGAGGACTACATTAAGTCAGGAATTCTTCTTGCCTGTGG
CATAGTGAACTCTGGGGTCCGGAATGAGTGTGTCCCTGCTCTGGGACTGCTTTCAGACTATGTTCTCCACAACAGCAACA
CCATGAGACTTGGTTCCATCTTTGGGTTAGGCTTGGCCTACGCTGGGGCT

Alignment

ORF - retro_ggor_486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.4 %
• Parental protein coverage: 55.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVAAEMEDGGRDKAPVQPQQSPAAGPGGTDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLVE-RLG
          AVAAEME.GG.DK..VQ.QQ.PAA.P.G.DEKPSGK.R.DAGDKDKEQELS.EDKQLQDELEMLVE...G
Retrocopy AVAAEMEEGGWDKMLVQSQQPPAAVPSGMDEKPSGKKRQDAGDKDKEQELSQEDKQLQDELEMLVE<MIG

Parental  EKDTSLYRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMAPGENKCFAADIISVLAMTMS
          EKDT.LYRPALEEL.RQIRSSTTSMT.V.KPLKFL.PHYGKLKEIYENMAPG.N..FAADIISVLAMTMS
Retrocopy EKDTFLYRPALEELQRQIRSSTTSMTLVTKPLKFLHPHYGKLKEIYENMAPGKNEHFAADIISVLAMTMS

Parental  GERECLKYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQREPLLTLVKEIVPYNMAHNAEHEA
          GE.ECLKYRLVGSQ.ELASW.HEYVRHLAGEVAK.WQEL.DAEKVQ.EPLLTLVKEIVPYNMAH.AEHEA
Retrocopy GECECLKYRLVGSQKELASWSHEYVRHLAGEVAKDWQELGDAEKVQQEPLLTLVKEIVPYNMAHDAEHEA

Parental  CDLLMEIEQ-VDMLEKDIDENAYAKVCLYLTSCVNYVPEPENSALLRCALGVFRKFSRFPEALRLALMLN
          CDLLMEIEQ.VDMLEKDIDENAY.KVCLYLTSCVNYV.EPENS.LLRCALGVF.KFSRFP.ALRLALM.N
Retrocopy CDLLMEIEQ<VDMLEKDIDENAYTKVCLYLTSCVNYVSEPENSVLLRCALGVF*KFSRFPKALRLALMCN

Parental  DMELVEDIFTSCKDVVVQKQMAFMLGRHGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPK
          DMELVEDIFTSCKDVVVQKQMAFMLG.HGVFLELSEDVEEYE.LTEIMSNVQLNS.FLALARELDI.EPK
Retrocopy DMELVEDIFTSCKDVVVQKQMAFMLGWHGVFLELSEDVEEYEHLTEIMSNVQLNSDFLALARELDILEPK

Parental  VPDDIYKTHLENNRFGGSGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAAS
          VPDDIYKTHLENNRFGGSGSQVDSA.MNLASSFVNGFVNAAF..DKLLTDDGNKWLYKNKDHGMLSAAAS
Retrocopy VPDDIYKTHLENNRFGGSGSQVDSACMNLASSFVNGFVNAAFV*DKLLTDDGNKWLYKNKDHGMLSAAAS

Parental  LGMILLWDVDGGLTQIDK-YLYSSEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLGSI
          .GM.LLWDVDGGL.QIDK..LYSSEDYIKSG.LLACGIVNSGVRNEC.PAL.LLSDYVLHNSNTMRLGSI
Retrocopy VGMLLLWDVDGGLIQIDK>NLYSSEDYIKSGILLACGIVNSGVRNECVPALGLLSDYVLHNSNTMRLGSI

Parental  FGLGLAYAGS
          FGLGLAYAG.
Retrocopy FGLGLAYAGA

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	0.29 RPM	183.90 RPM
SRP007412_cerebellum	0.16 RPM	108.38 RPM
SRP007412_heart	0.00 RPM	88.71 RPM
SRP007412_kidney	0.00 RPM	125.90 RPM
SRP007412_liver	0.00 RPM	57.87 RPM
SRP007412_testis	0.10 RPM	226.99 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_486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_486 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_531
Pan troglodytes	retro_ptro_397
Pongo abelii	retro_pabe_218

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175166	1 retrocopy	retro_hsap_531,
Gorilla gorilla	ENSGGOG00000027136	1 retrocopy	retro_ggor_486 ,
Mus musculus	ENSMUSG00000006998	2 retrocopies	retro_mmus_209, retro_mmus_3247,
Nomascus leucogenys	ENSNLEG00000006305	1 retrocopy	retro_nleu_1786,
Pongo abelii	ENSPPYG00000014354	1 retrocopy	retro_pabe_218,
Pan troglodytes	ENSPTRG00000015689	1 retrocopy	retro_ptro_397,