RetrogeneDB ID: retro_pabe_3334

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:57827567..57828742(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000018599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSPPYG00000005820
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 6 [Source:HGNC Symbol;Acc:9553]

Sequence

>retro_pabe_3334
CTTCTCATCATGGCGGACCCTAGCGATAAGGCGCTTCAGGACTACCGCAAGAAGCTGCTTGAGCACAAGGAGATCGACGG
CCGTTTTAAGGAGTTAAGGGAACAATTAAAAGAACTTACCAAGCAGTATGAAAAGTCTGAAAATGATCTGAAGGCCCTAC
AAAGTGTTGGGCAGATTGTGGGTGAAGTGCTTAAACAGTTAACTGAAGAAAAATTCATTGTTAAAGCTACCAATGGACCA
AGATACGTTGTGGGTTGTCGTCGACAGCTTGACGAAAGTAAGCTGAAGCCAGGAACAAGAGTTGCTTTGGATGTGACTAC
ACTAACTATCATGAGATATTTGCCAAGAAAGGTGGATCCACTGGTTTATAACATGTCTCATGAGGACCCTGGGAATGTTT
CTTATTCTGAGATTGGAGGGCTATCAGAACATATCCGGGAATTAAGAGAGGTGATAGAATTACCTCTTACAAACCCAGAG
TTATTTCAGCGTGTAGGAATAATACCTCCAAAAGGCTGTTTGTTATATGGACCACCAGTACGGGAAAAACACTCTTGGCA
CGAGCCGTTGCCAGCCAGCTGGACTGCAATTTCTTAAAGGTTGTATCTAGTTCTATTGTAGACAAGTACATTGGTGAAAG
TGCTCGTTTGATCAGAGAAATGTTTAATTATGCTAGAGATCATCAACTATGCATCATTTTTATGGATGAAATAGATGCTA
TTGGTGGTCGTCGGTTTTCTGAGGGTACTTCAGCTGACAGAGAGATTCAGAGAACGTTAATGGAGTTACTGAATCAAATG
GATGGATTTGATACTCTGCATAGAGTTAAAATGATCATGGCTACAAACAGACCAGATACACTGGATCCTGCTTTGCTGCA
TCCAGGAAGATTAGGTAGAAAAATACATATTGATTTACCAAATGAACAAGCAAGATTAGACATACTGAAAATCCATGCAG
GTCCCATTACAAAGCACGGTGAAATAGATTATGAAGCAATTGTGAAGCTTTCAGATGGCTTTAATGGAGCAGACCTGAGA
AATGTTTGTACTGAAGCAAATATGTTCGCAATTCGTGCTGATCATGATTTTGTAGTACAGGAAGACTTCATGAAAGCAGT
CAGAAAAGTGGCTGATTCTAAGAAGCTGGAGTCTAAATTGGACTACAAACCTGTG

Alignment

ORF - retro_pabe_3334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.95 %
• Parental protein coverage: 97.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLIMADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEE
          LLIMADP.DKALQDYRKKLLEHKEIDGR.KELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEE
Retrocopy LLIMADPSDKALQDYRKKLLEHKEIDGRFKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEE

Parental  KFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGG
          KFIVKATNGPRYVVGCRRQLD.SKLKPGTRVALD.TTLTIMRYLPR.VDPLVYNMSHEDPGNVSYSEIGG
Retrocopy KFIVKATNGPRYVVGCRRQLDESKLKPGTRVALDVTTLTIMRYLPRKVDPLVYNMSHEDPGNVSYSEIGG

Parental  LSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPP-GTGKTLLARAVASQLDCNFLKVVSSSIVDK
          LSE.IRELREVIELPLTNPELFQRVGIIPPKGCLLYGPP..TGKTLLARAVASQLDCNFLKVVSSSIVDK
Retrocopy LSEHIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPP<STGKTLLARAVASQLDCNFLKVVSSSIVDK

Parental  YIGESARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMI
          YIGESARLIREMFNYARDHQ.CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMI
Retrocopy YIGESARLIREMFNYARDHQLCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMI

Parental  MATNRPDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNV
          MATNRPDTLDPALL.PGRL.RKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNV
Retrocopy MATNRPDTLDPALLHPGRLGRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNV

Parental  CTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV
          CTEA.MFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV
Retrocopy CTEANMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV

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	0.06 RPM	26.54 RPM
SRP007412_cerebellum	0.12 RPM	36.24 RPM
SRP007412_heart	0.06 RPM	26.79 RPM
SRP007412_kidney	0.00 RPM	24.53 RPM
SRP007412_liver	0.03 RPM	26.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3334 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3334 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4059
Pan troglodytes	retro_ptro_2752
Gorilla gorilla	retro_ggor_2727

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334 , retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,