RetrogeneDB ID: retro_ptro_1409

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:60228521..60228767(+)
• Located in intron of: ENSPTRG00000013720

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPH3
• Ensembl ID: ENSPTRG00000014671
• Aliases: None
• Description: diphthamide biosynthesis 3 [Source:HGNC Symbol;Acc:27717]

Sequence

>retro_ptro_1409
ATGGCAGTATTTCATGACGAGGTGGAAATCGAGGACTTCCAATATGACGAGGACTCGGAGACATATTTCTGTCCCTGCCC
ATGCGGAGATAACTTCTCCATCACCAAGGAAGAGCTGGAGAATGGGGAAGGTGTGGCAATGTGTCCAGGCTGCTCTCTCA
TTATAAAAGTGATTTATGACAAAGATCAGTTTGCGTGTGGAGAAACAGTGCCAGTGCCTTCAGTCAACAAAGAATGAGTT
AAATGC

Alignment

ORF - retro_ptro_1409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETYFYPCPCGDNFSITKEDLENGEDVATCPSCSLIVKVIYDKDQFVCGETV
          MAVFHDEVEIEDFQYDEDSETYF.PCPCGDNFSITKE.LENGE.VA.CP.CSLI.KVIYDKDQF.CGETV
Retrocopy MAVFHDEVEIEDFQYDEDSETYFCPCPCGDNFSITKEELENGEGVAMCPGCSLIIKVIYDKDQFACGETV

Parental  PAPSANKELVKC
          P.PS.NKE.VKC
Retrocopy PVPSVNKE*VKC

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	0.77 RPM	4.95 RPM
SRP007412_cerebellum	0.32 RPM	5.27 RPM
SRP007412_heart	0.85 RPM	6.82 RPM
SRP007412_kidney	0.65 RPM	6.07 RPM
SRP007412_liver	0.16 RPM	5.14 RPM
SRP007412_testis	0.42 RPM	9.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1409 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1409 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2438
Gorilla gorilla	retro_ggor_174
Pongo abelii	retro_pabe_1795

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409 ,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,