RetrogeneDB ID: retro_ptro_1187

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:59242963..59243225(+)
• Located in intron of: ENSPTRG00000009486

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000011709
• Aliases: None
• Description: None

Sequence

>retro_ptro_1187
ATATTTGGGAAATATGGACCTATTCATCAAATCAGAGTGGAGAACACACCTGAAACTAGAGGAACAGCTTATGTGGTCTA
TGAAGACATCTTTGTTGCCAAGAATGCTTGTGATCACCTATCGGGATTCAATTTTTGTGACAGATAACTTGTGGTTTTGT
ACTATAATGCCAACAGGGCATTTCAGAAGATGGACACGAAGAAGGAGGAACAGCTGAAGCTTCTCACGGAGAAATATGGT
TGTCAAGATAGATCCACCAAAA

Alignment

ORF - retro_ptro_1187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 70.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKE
          IFGKYGPI.QIRV.NTPETRGTAYVVYEDIF.AKNACDHLSGFN.C.R.LVVLYYNANRAFQKMDTKK.E
Retrocopy IFGKYGPIHQIRVENTPETRGTAYVVYEDIFVAKNACDHLSGFNFCDR*LVVLYYNANRAFQKMDTKK-E

Parental  EQLKLLKEKYG-INTDPPK
          EQLKLL.EKYG....DPPK
Retrocopy EQLKLLTEKYG>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	0.07 RPM	12.23 RPM
SRP007412_cerebellum	0.04 RPM	12.51 RPM
SRP007412_heart	0.03 RPM	22.12 RPM
SRP007412_kidney	0.08 RPM	26.99 RPM
SRP007412_liver	0.03 RPM	21.96 RPM
SRP007412_testis	0.00 RPM	18.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1187 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1187 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1773
Pongo abelii	retro_pabe_1461

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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,