RetrogeneDB ID: retro_ptro_2869

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:5162816..5163485(-)
• Located in intron of: ENSPTRG00000020744

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDSS1
• Ensembl ID: ENSPTRG00000002374
• Aliases: None
• Description: prenyl (decaprenyl) diphosphate synthase, subunit 1 [Source:HGNC Symbol;Acc:17759]

Sequence

>retro_ptro_2869
AAAAGGAAAACACACAAGATCTGGGGTGAAAAGAAGGCTGTCCTTGCTGGAGATTTAATTCTTTCTGTAGTATCTACAGG
TGGGGCACAAACTGGAAATACAGCTGTTATATCTATTTTAACCCGAGTTATTGAAGATTTGGTGTGTGGTGAATTTCTTC
AGCTCGGGTCAAAAGAAAATCAGCATGAAAGATTTGCACAATACCTTGAAAAGACCTTCAAGAATACTGCGAGCCTGATA
GCCAGCAGTTGTAAAGCAGTCTCTGTTCTAGGATGCCCCAACCCAGTGGTGCATGAGATCTCCTATCAGTACGGAAAAAA
TGTAGGAATAGCTTTTCAGCTAATAGATGATGTATTCGACTTCACCTCATGTTCTAACATAGGCAAACCAGCATCAGCTG
ATGTGAATCTCAGGTTAGCCACTGGTCCTGTCCTGTTTGCCTGTCAGCAGTTCCCAGAAATGAATGCTATGATCATGAGA
TGGTTCAGTTTGCCGGGAGATGTAGACAGAGTTCCACAGTATGTATTACAGAGTGATGGTGTGCAACAAACAACCTACCT
TGCCCAGCAGTACTGCCATGAAGCAATAAGAGAGAGCAGTAAACTTCGACCATCCCCAGAAATAGACGCCCTCATTCAAC
TTTCAGAAATTGTACTCACAAGACATAAA

Alignment

ORF - retro_ptro_2869 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 54.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVRGEFLQLGSKENENERFAHYLE
          K....KIWGEKKAVLAGDLILS..S...A..GNT.VISILT.VIEDLV.GEFLQLGSKEN..ERFA.YLE
Retrocopy KRKTHKIWGEKKAVLAGDLILSVVSTGGAQTGNTAVISILTRVIEDLVCGEFLQLGSKENQHERFAQYLE

Parental  KTFKKTASLIANSCKAVSVLGCPDPVVHEIAYQYGKNVGIAFQLIDDVLDFTSCSDQMGKPTSADLKLGL
          KTFK.TASLIA.SCKAVSVLGCP.PVVHEI.YQYGKNVGIAFQLIDDV.DFTSCS...GKP.SAD..L.L
Retrocopy KTFKNTASLIASSCKAVSVLGCPNPVVHEISYQYGKNVGIAFQLIDDVFDFTSCSN-IGKPASADVNLRL

Parental  ATGPVLFACQQFPEMNAMIMRRFSLPGDVDRARQYVLQSDGVQQTTYLAQQYCHEAIREISKLRPSPERD
          ATGPVLFACQQFPEMNAMIMR.FSLPGDVDR..QYVLQSDGVQQTTYLAQQYCHEAIRE.SKLRPSPE.D
Retrocopy ATGPVLFACQQFPEMNAMIMRWFSLPGDVDRVPQYVLQSDGVQQTTYLAQQYCHEAIRESSKLRPSPEID

Parental  ALIQLSEIVLTRDK
          ALIQLSEIVLTR.K
Retrocopy ALIQLSEIVLTRHK

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	0.07 RPM	2.38 RPM
SRP007412_cerebellum	0.04 RPM	7.60 RPM
SRP007412_heart	0.03 RPM	1.95 RPM
SRP007412_kidney	0.05 RPM	3.53 RPM
SRP007412_liver	0.07 RPM	3.80 RPM
SRP007412_testis	0.11 RPM	13.07 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2869 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2869 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1157

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004695	1 retrocopy	retro_cjac_831,
Macaca mulatta	ENSMMUG00000005076	1 retrocopy	retro_mmul_1157,
Nomascus leucogenys	ENSNLEG00000016836	1 retrocopy	retro_nleu_2480,
Pan troglodytes	ENSPTRG00000002374	1 retrocopy	retro_ptro_2869 ,