RetrogeneDB ID: retro_ptro_1608

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:66403192..66403809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB12
• Ensembl ID: ENSPTRG00000002613
• Aliases: None
• Description: None

Sequence

>retro_ptro_1608
AAGCAGTATGACCACGTGGGCGATAACAGGAGCCAGGCAGTCAGGTCCAGCATCGTCATGGGGACTTCCACCATGGCTTT
GAGGCTGACATCTCCCCTGAAGACCTCTTCAACATGTTCTTTGGCAATGGCTTCCCTTCTAGTAAAGTCTACGTCTGCAG
CAATGGCTGCATGCGCTATACCTACCAGCAAAGGCAGGGCCGCAGGGAGAAGCGGAGTGACGGCAGCTTGCGGGTGTTTG
TGCAGCTGATACCCATCCTCATCCTCATGTCAGCTCTCAGCCAGCTCATGGTCTCCAGTCCACCCTACAGTTTGAGCCCA
AGACTGTTTGTGGGCCACATCACAGGCGAGTCACTGACCACCTGAGTGTCATCTACTATGTGGCAGGCATTTTCTCCGAG
GAGTACACAGGCTCCAGCCTCCAAACAGTCAAACCGAATGTGAAAGATGATTATATCGCCAACCTCTGGAACAACTGCTG
GACGGAGAAGCAGCAGACGAAAGGCTTGCTGTACCGAGGCCGCTACTTTGGTGACACAGATATGTACCACAAAGCACAGA
AGATGGGCAGCCCCCTGCTGCAGCCAGCTGTCACAGGATCAGGCCTCCCTGCATGGA

Alignment

ORF - retro_ptro_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.78 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KQYDQFGDDKSQAARHG-HGHGDFHRGFEADISPEDLFNMFFGGGFPSSNVHVYSNGRMRYTYQQRQDRR
          KQYD..GD..SQA.R...H.HGDFH.GFEADISPEDLFNMFFG.GFPSS.V.V.SNG.MRYTYQQRQ.RR
Retrocopy KQYDHVGDNRSQAVRSS<HRHGDFHHGFEADISPEDLFNMFFGNGFPSSKVYVCSNGCMRYTYQQRQGRR

Parental  DNQGDGGLGVFVQLMPILILILVSALSQLMVSSPPYSLSPRPSVGHI-HRRVTDHLGVVYYVGDTFSEEY
          ....DG.L.VFVQL.PILIL...SALSQLMVSSPPYSLSPR..VGHI.HRRVTDHL.V.YYV...FSEEY
Retrocopy EKRSDGSLRVFVQLIPILILM--SALSQLMVSSPPYSLSPRLFVGHI<HRRVTDHLSVIYYVAGIFSEEY

Parental  TGSSLKTVERNVEDDYIANLRNNCWKEKQQKEGLLYRARYFGDTDMYHKAQKMGT-PSCSRLSEVQASLH
          TGSSL.TV..NV.DDYIANL.NNCW.EKQQ..GLLYR.RYFGDTDMYHKAQKMG..P.CS.LS..QASLH
Retrocopy TGSSLQTVKPNVKDDYIANLWNNCWTEKQQTKGLLYRGRYFGDTDMYHKAQKMGS>PCCSQLSQDQASLH

Parental  G
          G
Retrocopy G

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	0.16 RPM	30.55 RPM
SRP007412_cerebellum	0.22 RPM	38.68 RPM
SRP007412_heart	0.03 RPM	16.38 RPM
SRP007412_kidney	0.05 RPM	51.94 RPM
SRP007412_liver	0.07 RPM	37.15 RPM
SRP007412_testis	0.00 RPM	69.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1608 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1608 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2273
Gorilla gorilla	retro_ggor_1691
Pongo abelii	retro_pabe_1945
Callithrix jacchus	retro_cjac_1200

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007303	1 retrocopy	retro_cjac_1200,
Dasypus novemcinctus	ENSDNOG00000009977	1 retrocopy	retro_dnov_866,
Homo sapiens	ENSG00000148719	1 retrocopy	retro_hsap_2273,
Gorilla gorilla	ENSGGOG00000000683	1 retrocopy	retro_ggor_1691,
Macropus eugenii	ENSMEUG00000002024	2 retrocopies	retro_meug_1115, retro_meug_1511,
Pongo abelii	ENSPPYG00000002353	1 retrocopy	retro_pabe_1945,
Pan troglodytes	ENSPTRG00000002613	1 retrocopy	retro_ptro_1608 ,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,