RetrogeneDB ID: retro_pabe_2400

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:195827324..195827770(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PERP
• Ensembl ID: ENSPPYG00000017043
• Aliases: None
• Description: PERP, TP53 apoptosis effector [Source:HGNC Symbol;Acc:17637]

Sequence

>retro_pabe_2400
CAGCTCCATCGCCTTCACCATCGTGGCAATGCCCAGGATGGCGGCAGCAGGCCCACCCAGGATGGTTGCCAGAGCCTCGT
GGAGTACGTAGGAGGAAAAGCAGCCGCTGCCATGCTCTTCTGTGGCTGTATCATGCTGGTGACCTGTTTCATCCTCACCT
TCTTTGCCCTCTGTGCACCCCCGATGCTAGTCCTCCTAAGGGTGAGTTGGAGGCCTCCCTACCCCGGCTGCTGTGTTGCA
GATCATCTCCCTGGTAATTAACCCTGTGAAGTATACCCATACCTTCAATCTTCATGCCAACCCCGCCGTCACATCACATC
TGTCACTGGACCTGCGGCTTCCAGTGGGTGGACACAATTATCCTGATTGGCTGTCCTTTCTCCTTCTGCTGCAGCGCGAA
GGACGAAGACAACCTCCTGTGAGGCGCCAAGCCCAGGTACTTCCAC

Alignment

ORF - retro_pabe_2400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.53 %
• Parental protein coverage: 76.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTSSLWWKCSQEGGGSGSYEEGCQSLMEYAWGKTAAAMLFWGFLILV-NLFHPXXLRPLWTPDAR-LLRV
          Q...L........GGS.....GCQSL.EY..GK.AAAMLF.G...LV..LFHP..L.PL.TPDA..LLRV
Retrocopy QLHRLHHRGNAQDGGSRPTQDGCQSLVEYVGGKAAAAMLFCGCIMLV<DLFHPHLLCPLCTPDAS>LLRV

Parental  -IGGLLALAAVFQIISLVIYPVKYTQTFALHANPAVT-YIYNWAYGFGWAATIILIGCAFFFCCLPNYED
          ..GGL...AAV.QIISLVI.PVKYT.TF.LHANPAVT..I..W..GF.W..TIILIGC.F.FCC....ED
Retrocopy >VGGLPTPAAVLQIISLVINPVKYTHTFNLHANPAVT>HICHWTCGFQWVDTIILIGCPFSFCCSAKDED

Parental  DLLGNAKPRYFY
          .LL..AKPRYF.
Retrocopy NLL*GAKPRYFH

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	2.88 RPM
SRP007412_cerebellum	0.00 RPM	7.66 RPM
SRP007412_heart	0.00 RPM	46.09 RPM
SRP007412_kidney	0.00 RPM	30.73 RPM
SRP007412_liver	0.00 RPM	16.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2400 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2400 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2901

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020097	1 retrocopy	retro_btau_165,
Callithrix jacchus	ENSCJAG00000019024	1 retrocopy	retro_cjac_3992,
Homo sapiens	ENSG00000112378	2 retrocopies	retro_hsap_1523, retro_hsap_2901,
Gorilla gorilla	ENSGGOG00000028340	1 retrocopy	retro_ggor_1165,
Macropus eugenii	ENSMEUG00000004872	1 retrocopy	retro_meug_845,
Microcebus murinus	ENSMICG00000013979	1 retrocopy	retro_mmur_353,
Myotis lucifugus	ENSMLUG00000001473	1 retrocopy	retro_mluc_2287,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156,
Nomascus leucogenys	ENSNLEG00000014930	2 retrocopies	retro_nleu_1934, retro_nleu_631,
Oryctolagus cuniculus	ENSOCUG00000004238	1 retrocopy	retro_ocun_170,
Otolemur garnettii	ENSOGAG00000011669	1 retrocopy	retro_ogar_631,
Pongo abelii	ENSPPYG00000017043	3 retrocopies	retro_pabe_1267, retro_pabe_2400 , retro_pabe_2416,