RetrogeneDB ID: retro_ptro_205

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:134097181..134098039(+)
• Located in intron of: ENSPTRG00000001433

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD7
• Ensembl ID: ENSPTRG00000008343
• Aliases: None
• Description: None

Sequence

>retro_ptro_205
GATCTGGTGGTGCAGAAGGTGGTGGTCCACCCCCAGGTACTGCTCAATGTGGTGGATCATTTCAACAGAATCAGCAAGGT
TGGAAACCAGAAATGCACTCTTCATGTGCTTTTGCGGTCATGGCAAATGAAAGTACTTGATGTATCCAGCAGTTTTACAG
TCCCTTTTAATGAAGATGACAAAGATAATTGTTTTTTAGCCCACGATTATTTGAAAAACACATACAGAATGTTTAAGAGG
GTGAATGCCAGGGAAAGAATAGTTGAGTGGTACCACATAGGCCCTAAACTACACAAGAATGACACTGCCTTCGATGAAAT
CATGAAAAGATACTGCCGTAACTCAGTATTGGTCACTAGTGACATGAAGCCAAAGGACTTAGGGCTGCCCACAGAAGCAT
ATATTTCAGTAGAAGTCTATGAAGATGGAACTTCAGCCTTGAAAACATTTGAGCATGTGACCAGTGAAACTGGAGCAGAG
GAAGCTAAGGAAATTGGAGTTAAACACTTGTTACAAGACATCAAAGACACTACAGTGGGCACTCTTTCCCAGTGTATCAC
AAACCAGGTCCTGGATTTGAAGGGACTGAACTCCAAGCTTCTGGGTACCAGAAGCTACCTGGAAAAAGTTGCCACAGGCA
AACTGTCCACCAACCACCGATTCATCTATCAGCTGCAGGTCTTCAAGCTGCTGCCAGTCATTAGCCTATAGGAGTTTGTC
AAGGCCTTTTACCTGAAGACCAATAACCAAATGGTAGCAGTGTACTTGGCCTCGCCGATCCATTCTGTGATCACCCTACA
CAACCTCATCAACAAGACTGCCAACTGGGATGCAGAGAAGAAAGACAGGAAAAAGAAA

Alignment

ORF - retro_ptro_205 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.6 %
• Parental protein coverage: 89.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFLDH
          .L.VQKVVVHP.VLL.VVDHFNRI.KVGNQK....VLL.SWQ.KVLDVS.SF.VPF.EDDKD....FL.H
Retrocopy DLVVQKVVVHPQVLLNVVDHFNRISKVGNQKCTLHVLLRSWQMKVLDVSSSFTVPFNEDDKDNC--FLAH

Parental  DYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYISVE
          DYL.N.Y.MFK.VNARERIV.WYH.GPKLHKND.A..E.MKRYC.NSVLV..D.KPKDLGLPTEAYISVE
Retrocopy DYLKNTYRMFKRVNARERIVEWYHIGPKLHKNDTAFDEIMKRYCRNSVLVTSDMKPKDLGLPTEAYISVE

Parental  EVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLLDIRSYL
          .V..DGT...KTFEHVTSE.GAEEA.E.GV.HLL.DIKDTTVGTLSQ.ITNQV..LKGLNSKLL..RSYL
Retrocopy -VYEDGTSALKTFEHVTSETGAEEAKEIGVKHLLQDIKDTTVGTLSQCITNQVLDLKGLNSKLLGTRSYL

Parental  EKVATGKLPINHQIIYQLQDVFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIAN
          EKVATGKL..NH..IYQLQ.VF.LLP..SL.EFVKAFYLKTN.QMV.VYLAS.I.SV..LHNLI.NK.AN
Retrocopy EKVATGKLSTNHRFIYQLQ-VFKLLPVISL*EFVKAFYLKTNNQMVAVYLASPIHSVITLHNLI-NKTAN

Parental  RDAEKKEGQEK
          .DAEKK....K
Retrocopy WDAEKKDRKKK

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	0.09 RPM	67.82 RPM
SRP007412_cerebellum	0.00 RPM	65.50 RPM
SRP007412_heart	0.00 RPM	88.05 RPM
SRP007412_kidney	0.31 RPM	57.82 RPM
SRP007412_liver	0.10 RPM	78.69 RPM
SRP007412_testis	0.00 RPM	110.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_205 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_205 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_205 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_234
Pongo abelii	retro_pabe_418
Macaca mulatta	retro_mmul_417

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205 ,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,