RetrogeneDB ID: retro_ptro_2702

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:82786764..82787425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSPTRG00000019553
• Aliases: None
• Description: None

Sequence

>retro_ptro_2702
ACAGACATTGAGGCAGGGATGAAATTTGATGTGGAAGAATGTAAGTATTAAATTCATATTCCCATACTTTCTAAGATTGA
TCCAACAATTACCATGATGCCGGTGGAGTAAAAACCTGATGTCATATACAGTGATGTTGTTGGCTGTAGGGAACAGATTG
AGACATTGTAAGCAGTTGAAACCCCACTACTTCATCCAGAGAGATTTGTTAACCTTGGCGTGGAGCCTCCCAAGAGTGTG
CTCTTTGGTCCACTAGGTGCAAGACACTCTGTGCTTAGGTGGTTGCTAAATAGGACTGATGCTTGCTTCATCGAGTTATT
GGATATTAACTTTTACAGAAATATATCTGCAAAGGGGCTGGAATGGTTCATGAGCTCTTCCCAATGGCCAGAACAAGAAA
CGCCTGCCTTATCTTCTTTGATGAAACTGATGCTATTGGAAGAGCTCAGTTTGATGATGGTGCTGGAGGTGACAATGAAG
TACAGAGAAAAATGTGGGAACTAATTCATCAGTTGGATGGCTTTGACCCTCAAGGCAATATTAAGTGCTGATGGCCACTA
ACAGACCTGATACTTTGGATTCAGCACTGATGAAGCCAGGGAAATTGGATAGAAAGATTGAGTTTAGTTTACCTGATCTA
GAGGGTCAGACTCACATCTTT

Alignment

ORF - retro_ptro_2702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.89 %
• Parental protein coverage: 51.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERF
          TDIE.GM...V...KY.IHIP...KIDPT.TMM.VE.KPDV.YSDV.GC.EQIE.L...VETPLLHPERF
Retrocopy TDIEAGMKFDVEECKY*IHIPILSKIDPTITMMPVE*KPDVIYSDVVGCREQIETL-*AVETPLLHPERF

Parental  VNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFI-RVIGSELVQKYVGEGARMVRELFEMARTKKAC
          VNLG.EPPK.V.LFGP.G.......R...NRTDACFI.RVIG..L.QKY...GA.MV.ELF.MART..AC
Retrocopy VNLGVEPPKSV-LFGPLGARHSV-LRWLLNRTDACFI<RVIGY*LLQKYICKGAGMVHELFPMARTRNAC

Parental  LIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIK-VLMATNRPDTLDPALMRPGRLDR
          LIFFDE.DAIG.A.FDDGAGGDNEVQR.M.ELI.QLDGFDP.GNIK.VLMATNRPDTLD.ALM.PG.LDR
Retrocopy LIFFDETDAIGRAQFDDGAGGDNEVQRKMWELIHQLDGFDPQGNIK<VLMATNRPDTLDSALMKPGKLDR

Parental  KIEFSLPDLEGRTHIF
          KIEFSLPDLEG.THIF
Retrocopy KIEFSLPDLEGQTHIF

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	0.04 RPM	42.11 RPM
SRP007412_cerebellum	0.00 RPM	68.00 RPM
SRP007412_heart	0.00 RPM	72.40 RPM
SRP007412_kidney	0.03 RPM	56.33 RPM
SRP007412_liver	0.00 RPM	70.38 RPM
SRP007412_testis	0.00 RPM	104.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2702 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2702 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3980
Gorilla gorilla	retro_ggor_2672

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702 ,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,