RetrogeneDB ID: retro_pabe_2788

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:149498264..149498543(-)
• 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_2788
AAACAAAAATATCAAAAACTCATATTAATGTATCATCCAGATAAACAAAGTACAGATGTACCAGCAGGAACAGTGGAGGA
ATGTGTACAGAAGTTCATCGAAATTGATCAAGCATGGAAAATTCTAGGAAATGAAGAGACAAAAAGAGAGTATGACCTGC
AGCGGTGTGAAGACGACCTAAGAAATGTAGGACCAGTAGATGCTCAAGTGTATCTTAAAGAAATGTCTTGGAATGAAGCT
GATCACTCTTTTTATCTGAGTTGCAGATGTGGTGGAAAA

Alignment

ORF - retro_pabe_2788 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.85 %
• Parental protein coverage: 62.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQAWKILGNEETKREYDLQRCEDDLRNVGPVDAQV
          KQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQAWKILGNEETKREYDLQRCEDDLRNVGPVDAQV
Retrocopy KQKYQKLILMYHPDKQSTDVPAGTVEECVQKFIEIDQAWKILGNEETKREYDLQRCEDDLRNVGPVDAQV

Parental  YLEEMSWNEGDHSFYLSCRCGGK
          YL.EMSWNE.DHSFYLSCRCGGK
Retrocopy YLKEMSWNEADHSFYLSCRCGGK

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_2788 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2788 has 0 orthologous retrocopies within eutheria group .

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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,