RetrogeneDB ID: retro_pabe_2783

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:135159797..135160234(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC24
• Ensembl ID: ENSPPYG00000003390
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 24 [Source:HGNC Symbol;Acc:26979]

Sequence

>retro_pabe_2783
ATAATGGCATTTGAGATGATGCCAAAAAATAATTGGTATAGCATTTTGGGGGGCAGACCGAAATGTGTCAAACTTAAAAC
AAAAGTATAAAAAATTTATATTAAAGTATCATTCAGATTAACAAAGTACAGATGTGCCAGCAGGAATAGTGGAGGACTGT
ATACAGAAATTCATTGAAATTGATCAGGCATGGAAAATTCCAGGGAATGAAGAGAAAAAAAGAGTATGACCCTCAGTGGC
ATGAAGATGATCTAAGAAATATGGAACCAGTAGATGCTCAACTATATCTTGAAAAAGTGTCTTGGAAAAAAGATGATGAC
TCTTTTTCCCCAAGTTGCCAATGTGGTAGAAAACACAGTGTTTCCAAGGATGAAGCAGAAGAAGTTAACCTATTTTCTTG
TGATACATGTTCACTAATTACAGAACTTCTTCATTAT

Alignment

ORF - retro_pabe_2783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.67 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMAVEQMPKKDWYSIL-GADPSANISDLKQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQAW-KI
          .MA.E.MPK..WYSIL.GAD...N.S.LKQKY.K.IL.YH.D.QSTDVPAG.VE.C.QKFIEIDQAW.K.
Retrocopy IMAFEMMPKNNWYSIL>GAD--RNVSNLKQKYKKFILKYHSD*QSTDVPAGIVEDCIQKFIEIDQAW>KF

Parental  LGNEETKREYDLQRCEDDLRNVGPVDAQVYLEEMSWNEGDHSFYLSCRCGGKYSVSKDEAEEVSLISCDT
          .G....K.EYD.Q..EDDLRN..PVDAQ.YLE..SW...D.SF..SC.CG.K.SVSKDEAEEV.L.SCDT
Retrocopy QGMKR-KKEYDPQWHEDDLRNMEPVDAQLYLEKVSWKKDDDSFSPSCQCGRKHSVSKDEAEEVNLFSCDT

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	9.40 RPM
SRP007412_cerebellum	0.00 RPM	7.90 RPM
SRP007412_heart	0.00 RPM	4.49 RPM
SRP007412_kidney	0.00 RPM	3.94 RPM
SRP007412_liver	0.00 RPM	1.53 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2783 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2783 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2301
Macaca mulatta	retro_mmul_2112

---

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,