RetrogeneDB ID: retro_ptro_699

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:68233890..68235069(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSPTRG00000006352
• Aliases: None
• Description: None

Sequence

>retro_ptro_699
AAGCAGCTTCTCATCATGGTGGACTCTAGAGGTAAGGTGCTTCAGGACTACCGCAAGAAGCTGCTTGAGCACAAGATCGA
CGGCCGTCTTAACGAGTTAAGGGAACAATTAAAAGAACTTACCAAGCAGTATGAAAAGTCTGAAAATGATCTGAAGGCCC
TACAAAGTGTTGGACAGATTGTGGGTGAAGTGCTTCAACAGTTAACTGAAGCAAAATTCATTGTTAAAGCTACAAATGGA
CCAAGATGTGTTGTGGGTTGTCGTCGACAGCTTGACAAAAGTAAGCTGAAGCCAGGAACAGGAGTCGCTTTGGATATGAC
TACACTAACTATCATGAGATATTTGCCAAGAGAGGTGGATCCACTGGTTTATAACATGTCTCATGAGGACCCCTGGAATG
TTTCTTATTCTGAGATTGGAGGGCTATCGGAACAGATCTGGGAATTAAGAGAGGTGATAGAATTAGCTCTTACAAACCCA
GAGTTATTTCAGTGGGTAGGAATAATGCCTCCAAAATGCTGTTTGTTACACGGACCACCAGGTATGGGAAAAACACTCTT
GGCACAAGCTGTTGCTAGCCAGCTGGACTACAATTTCTTAAAGGTTGTATCTAGTTCTATTGTAGACAAGTACATTGGTG
AAAGTGCTTGTTTGATCAGAGAAATGTTTAATTATCCCAGGAACCATAAACCATGCATCATTTTTATGGATGAAATAGAT
GCTATTGGTGGTTGTCCGTTTTCTGAGGGTACTTCAGCTGACAGAGAGATTCAGAGTACTTCAATGGAGTTACTGAATCA
AATGGATGGATTTGATACTCTGCACAGAGTTAAAATGATCATGACTACAAACAGACCAGATACACTGGATCCTGCTTTGC
TGCATCCGGGAAGATTAGATAGAAAAATACATATTGATTTGCCAGATGAACAAGCAAGATTAGACCTACTGAAAATCCAT
GCAGGTCCCATTACAAAGCATGGTGAGAGAGATTAGGAAGCAATTGTGAAGCTTTCAGATGGCTTTAATGGAGTAGACCT
GAGAAATGTTTGTACTGAAGCAGGCATGTTCGCAATTCGTGCTGATCATGATTTTGTAGTACAGGAAGACTTCATGAAAG
CAGTCAGAAAAGTGGCTGATTCTGACAAGCTAGAGTCTAAATTGGACTACAAACCTATG

Alignment

ORF - retro_ptro_699 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.1 %
• Parental protein coverage: 97.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRLLIMADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLT
          ..LLIM.D.R.K.LQDYRKKLLEHK.IDGRL.ELREQLKELTKQYEKSENDLKALQSVGQIVGEVL.QLT
Retrocopy KQLLIMVDSRGKVLQDYRKKLLEHK-IDGRLNELREQLKELTKQYEKSENDLKALQSVGQIVGEVLQQLT

Parental  EEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEI
          E.KFIVKATNGPR.VVGCRRQLDKSKLKPGT.VALDMTTLTIMRYLPREVDPLVYNMSHEDP.NVSYSEI
Retrocopy EAKFIVKATNGPRCVVGCRRQLDKSKLKPGTGVALDMTTLTIMRYLPREVDPLVYNMSHEDPWNVSYSEI

Parental  GGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVD
          GGLSEQI.ELREVIEL.LTNPELFQ.VGI.PPK.CLL.GPPG.GKTLLA.AVASQLD.NFLKVVSSSIVD
Retrocopy GGLSEQIWELREVIELALTNPELFQWVGIMPPKCCLLHGPPGMGKTLLAQAVASQLDYNFLKVVSSSIVD

Parental  KYIGESARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKM
          KYIGESA.LIREMFNY.R.H.PCIIFMDEIDAIGG..FSEGTSADREIQ.T.MELLNQMDGFDTLHRVKM
Retrocopy KYIGESACLIREMFNYPRNHKPCIIFMDEIDAIGGCPFSEGTSADREIQSTSMELLNQMDGFDTLHRVKM

Parental  IMATNRPDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRN
          IM.TNRPDTLDPALL.PGRLDRKIHIDLP.EQARLD.LKIHAGPITKHGE.D.EAIVKLSDGFNG.DLRN
Retrocopy IMTTNRPDTLDPALLHPGRLDRKIHIDLPDEQARLDLLKIHAGPITKHGERD*EAIVKLSDGFNGVDLRN

Parental  VCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV
          VCTEAGMFAIRADHDFVVQEDFMKAVRKVADS.KLESKLDYKP.
Retrocopy VCTEAGMFAIRADHDFVVQEDFMKAVRKVADSDKLESKLDYKPM

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	32.39 RPM
SRP007412_cerebellum	0.04 RPM	18.64 RPM
SRP007412_heart	0.00 RPM	28.74 RPM
SRP007412_kidney	0.00 RPM	24.27 RPM
SRP007412_liver	0.00 RPM	16.83 RPM
SRP007412_testis	0.00 RPM	11.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_699 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_699 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_699 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_858

---

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,