RetrogeneDB ID: retro_ptro_3099

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:28078913..28079336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VKORC1
• Ensembl ID: ENSPTRG00000008031
• Aliases: None
• Description: Pan troglodytes vitamin K epoxide reductase complex subunit 1 (VKORC1), mRNA. [Source:RefSeq mRNA;Acc:NM_001251930]

Sequence

>retro_ptro_3099
GTCGCTCTATGCGCGCTGCACGTGAAGGCGGCGCGCGCCCGGGACCGGGATTACCGCGCTCTCTGCGACGTGGGCACCGC
CATTAGCTGTCCGCGCGTCTTCTCCTCCAGGTAGGGCAGGGGCTTCGGGCTGGTGGAGCACGTGCTGGGACAGGACAGCA
TCCTCAATCAATCCGATAACATATTCCCTTGCGTCTTGTACACAGTACAGTTGTTAGGTTGCCTGAGGACGCGCTGGGCC
TCTGTCCTGCGGCTGCTGAGCTCCCTGCTGTCTCTCGCTGGTTCTGTCTACCTGGCCTGAATTCTGTTCTTCGTGCTCTA
TGATTTCTGCATCGTTTGCATCACCACCTATGCCATCAACGTGGGCCTGATGTGGCTCAGTTTCCGGAAGCTCCAAGAAC
CCCAGGGCAAGGCTAAGAGGTAC

Alignment

ORF - retro_ptro_3099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 87.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQ
          ..L.ALHVKAARARDRDYRALCDVGTAISC.RVFSSR.GRGFGLVEHVLGQDSILNQS..IF.C..YT.Q
Retrocopy VALCALHVKAARARDRDYRALCDVGTAISCPRVFSSR*GRGFGLVEHVLGQDSILNQSDNIFPCVLYTVQ

Parental  LLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQEPQGKAK
          LL.GCLRTRWASVL.LLSSL.SLAGSVYLA.ILFFVLYDFCIVCITTYAINV.LMWLSFRK.QEPQGKAK
Retrocopy LL-GCLRTRWASVLRLLSSLLSLAGSVYLA*ILFFVLYDFCIVCITTYAINVGLMWLSFRKLQEPQGKAK

Parental  RH
          R.
Retrocopy RY

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	23.77 RPM
SRP007412_cerebellum	0.00 RPM	19.43 RPM
SRP007412_heart	0.00 RPM	11.63 RPM
SRP007412_kidney	0.00 RPM	38.26 RPM
SRP007412_liver	0.00 RPM	244.88 RPM
SRP007412_testis	0.00 RPM	15.18 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3099 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3099 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3099 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4664

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003097	1 retrocopy	retro_cjac_4049,
Homo sapiens	ENSG00000167397	1 retrocopy	retro_hsap_4664,
Oryctolagus cuniculus	ENSOCUG00000002289	1 retrocopy	retro_ocun_1423,
Ochotona princeps	ENSOPRG00000016146	3 retrocopies	retro_opri_1124, retro_opri_1164, retro_opri_70,
Pongo abelii	ENSPPYG00000007306	1 retrocopy	retro_pabe_3624,
Pan troglodytes	ENSPTRG00000008031	1 retrocopy	retro_ptro_3099 ,