RetrogeneDB ID: retro_ptro_2301

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:134376657..134377094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC24
• Ensembl ID: ENSPTRG00000003471
• Aliases: DNAJC24, DPH4, ZCSL3
• Description: None

Sequence

>retro_ptro_2301
ATAATGGCATTTGAGCTGATGCCAAAAAATAATTGGTATAGCATTTTTGGGGGCAGACCCAAATGTGTCAAACCTAAAAC
TAAAGTATGAAAAACTTGTATTAAAGCAGCATTCAGATTAACAAAGTACAGATGTGCCAGCAGGAATAGTGGAGGACTGT
ATACAGAAAGTCGTTGAAATTGATCAGGCATGGAAAATTCTAGGGAATGAAGAGAAAAAAAGAGTATGATACTCAGTGAC
ATGAAGATGATCTAAGAAATATGGAACCAATAGATGCTCAACTATATCTTGAAAAAGTGCCTTGGAAAAAAGATGATGAT
TCTTTTTCCCCAAGTTGCCAATGTGGTAGAAAACACAGTGTTTCCAAGGATGAAGCAGAGGAAGTTAACCTATTTTCTTG
TGATACATGTTCACTAATTACAGAACTTCTTCATTAT

Alignment

ORF - retro_ptro_2301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.33 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMAVEQMPKKDWYSI-LGADPSANISDLKQKYQKLILMYHPDKQSTDVPAGTVEECVQ-KFIEIDQAWKI
          .MA.E.MPK..WYSI.LGADP..N.S.LK.KY.KL.L..H.D.QSTDVPAG.VE.C.Q.K........K.
Retrocopy IMAFELMPKNNWYSI>LGADP--NVSNLKLKYEKLVLKQHSD*QSTDVPAGIVEDCIQ>KSLKLIRHGKF

Parental  LGNEETKREYDLQRCEDDLRNVGPVDAQVYLEEMSWNEGDHSFYLSCRCGGKYSVSKDEAEEVSLISCDT
          .G....K.EYD.Q..EDDLRN..P.DAQ.YLE...W...D.SF..SC.CG.K.SVSKDEAEEV.L.SCDT
Retrocopy *GMKR-KKEYDTQ*HEDDLRNMEPIDAQLYLEKVPWKKDDDSFSPSCQCGRKHSVSKDEAEEVNLFSCDT

Parental  CSLIIELLHY
          CSLI.ELLHY
Retrocopy CSLITELLHY

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	7.04 RPM
SRP007412_cerebellum	0.00 RPM	8.50 RPM
SRP007412_heart	0.00 RPM	9.27 RPM
SRP007412_kidney	0.00 RPM	8.42 RPM
SRP007412_liver	0.00 RPM	5.66 RPM
SRP007412_testis	0.00 RPM	22.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2301 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2301 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2783
Macaca mulatta	retro_mmul_2112

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013512	1 retrocopy	retro_dnov_2247,
Dipodomys ordii	ENSDORG00000000248	3 retrocopies	retro_dord_221, retro_dord_395, retro_dord_77,
Echinops telfairi	ENSETEG00000003054	1 retrocopy	retro_etel_161,
Microcebus murinus	ENSMICG00000007553	3 retrocopies	retro_mmur_1052, retro_mmur_1150, retro_mmur_973,
Macaca mulatta	ENSMMUG00000006845	1 retrocopy	retro_mmul_2112,
Nomascus leucogenys	ENSNLEG00000017878	1 retrocopy	retro_nleu_3029,
Otolemur garnettii	ENSOGAG00000007848	1 retrocopy	retro_ogar_1542,
Ochotona princeps	ENSOPRG00000001638	1 retrocopy	retro_opri_881,
Pongo abelii	ENSPPYG00000003390	2 retrocopies	retro_pabe_2783, retro_pabe_2788,
Pan troglodytes	ENSPTRG00000003471	1 retrocopy	retro_ptro_2301 ,
Tarsius syrichta	ENSTSYG00000009243	1 retrocopy	retro_tsyr_623,