RetrogeneDB ID: retro_ptro_3065

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393415.1:2950..3695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRAXIN
• Ensembl ID: ENSPTRG00000000150
• Aliases: None
• Description: dorsal inhibitory axon guidance protein [Source:HGNC Symbol;Acc:25054]

Sequence

>retro_ptro_3065
CCCTCCGCCTCCTCCCTGCCGACCCTAGTCCTAGTCCTCCTGCTGCCCCTGGAGCTGAGCCTGGCAAACGCCCTTGCACC
TGGGACCCCTGCTCAGAATCTACCCGAGAATCACATCGACCTCCCAGGCCCAGCGCTGTGGTCGCCTCAGGCCAGCCACC
ACCGCCAGCGGGGCCCGGGCAAGAAGGAGTGGCTCAGGCCTGCCCAGGGAGGCCCAGGATAGGGCTGTGCTCACCGCCAC
CAGGCAGGCTTACAGGCTGCCAGGGCCTGAGGGGCCGCTGCCTGAGCAGAGTCCTGCAGGCCTGCTGCGGGTCAAGGACC
TGCTCCTGGGGCTCGAGTTGCCCTACCCCAAGAAGGAGAATCGGTGTCCAGGGTGGTAGAGGGCCAGGAAACGCAGCAGG
GAGTACAAGAGACGCAGGGACAGGCTGAGGCTGCACCGAGGCCGAGCCTTGGTCGGAGGTCCCAGCTCCCTGATGAAGGC
GGAGCTCTCCGAAGCCAAGGCGCTGGATGCGACCATGGAGGATTCTTCCGCCGGTCTGGCCCCCACCATGCTCTTCCTCA
CCACCTTTGAGGCAGCACCTGCCACAGAAGAGTCCCTGATCCTGCTCATCGCCCCCCTGCGGCCCCAGGCACAGCGCAGG
CCTGACGGGGAGGTGATACCCACACTGGACGTGGCCTTGTTCGACTGGACCGATTATGAAGACTTAAAACCTGATGGCGG
GCCCTCTGCAAAGAAGAAAGAAAAA

Alignment

ORF - retro_ptro_3065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.66 %
• Parental protein coverage: 71.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAIHTAPMLFLILLLPLELSLAGALAPGTPARNLPENHIDLPGPALWTPQASHHRRRG-PGK-KEWGPGL
          P.....P.L.L.LLLPLELSLA.ALAPGTPA.NLPENHIDLPGPALW.PQASHHR.RG.PG.....G.GL
Retrocopy PSASSLPTLVLVLLLPLELSLANALAPGTPAQNLPENHIDLPGPALWSPQASHHRQRG<PGQ<RRSGSGL

Parental  PSQAQDGAVVTATRQASRLPEAEGLLPEQSPAGLLQDKDLLLGLALPYPEKENRPPGWERTRKRSREHKR
          P..AQD.AV.TATRQA.RLP..EG.LPEQSPAGLL..KDLLLGL.LPYP.KENR.PGW.R.RKRSRE.KR
Retrocopy PREAQDRAVLTATRQAYRLPGPEGPLPEQSPAGLLRVKDLLLGLELPYPKKENRCPGW*RARKRSREYKR

Parental  RRDRLRLHRGRALVRGPSSLMKKAELSEAQVLDAAMEESSTSLAPTMFFLTTFEAAPATEESLILPVTSL
          RRDRLRLHRGRALV.GPSSLM.KAELSEA..LDA.ME.SS..LAPTM.FLTTFEAAPATEESLIL....L
Retrocopy RRDRLRLHRGRALVGGPSSLM-KAELSEAKALDATMEDSSAGLAPTMLFLTTFEAAPATEESLILLIAPL

Parental  RPQQAQPRSDGEVMPTLDMALFDWTDYEDLKPDGWPSAKKKEK
          RP.QAQ.R.DGEV.PTLD.ALFDWTDYEDLKPDG.PSAKKKEK
Retrocopy RP-QAQRRPDGEVIPTLDVALFDWTDYEDLKPDGGPSAKKKEK

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	2.68 RPM
SRP007412_cerebellum	0.00 RPM	0.39 RPM
SRP007412_heart	0.00 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.08 RPM
SRP007412_liver	0.00 RPM	0.10 RPM
SRP007412_testis	0.00 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3065 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3065 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3065 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000162490	1 retrocopy	retro_hsap_4779,
Macaca mulatta	ENSMMUG00000001652	1 retrocopy	retro_mmul_2550,
Pongo abelii	ENSPPYG00000001884	1 retrocopy	retro_pabe_3719,
Pan troglodytes	ENSPTRG00000000150	1 retrocopy	retro_ptro_3065 ,