RetrogeneDB ID: retro_pabe_1461

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:51644421..51644680(+)
• Located in intron of: ENSPPYG00000008516

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000012603
• Aliases: None
• Description: None

Sequence

>retro_pabe_1461
ATATTTGGGAAATATGGACCTATTCATCAAATCAGAGTGGAGAGCACACCTGAAACTAGAGGAACAGCTTATGTGGTCTG
TGAAGACATCTTTGTTGCCAAGAATGCTTGTGATCATCTATCGGGATTCAATTTTTGTGACAGATAACTTGTGGTTTTGT
ACTATAATGCCAACAGGGCATTTCAGAAGATGGACATGAAGGAGGAACAGCTGAAGCTTCTCATGGAGAAATATGGTTGT
CAAGATAGATCCACCAAAA

Alignment

ORF - retro_pabe_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 70.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKE
          IFGKYGPI.QIRV..TPETRGTAYVV.EDIF.AKNACDHLSGFN.C.R.LVVLYYNANRAFQKMD...KE
Retrocopy IFGKYGPIHQIRVESTPETRGTAYVVCEDIFVAKNACDHLSGFNFCDR*LVVLYYNANRAFQKMD--MKE

Parental  EQLKLLKEKYG-INTDPPK
          EQLKLL.EKYG....DPPK
Retrocopy EQLKLLMEKYG>VKIDPPK

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	11.78 RPM
SRP007412_cerebellum	0.12 RPM	17.75 RPM
SRP007412_heart	0.03 RPM	15.29 RPM
SRP007412_kidney	0.07 RPM	21.48 RPM
SRP007412_liver	0.03 RPM	22.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1461 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1461 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1773
Pan troglodytes	retro_ptro_1187

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461 ,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,