RetrogeneDB ID: retro_ptro_2288

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:112828567..112828729(-)
• Located in intron of: ENSPTRG00000017133

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSBP1
• Ensembl ID: ENSPTRG00000008401
• Aliases: None
• Description: None

Sequence

>retro_ptro_2288
GTGGCTGAGACTGACCCCAAGATTGTGCAGGATCTCACATTGATGGTGGAGATGTTCCTGCAACATGTGTGAAATAAGTT
TCAGACCATGTCTGACCAGACCATTGGAAAAATTGATGATATGAATACTCTCATAGATCTTGAGAAAAACGTCAAAGATC
TC

Alignment

ORF - retro_ptro_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.45 %
• Parental protein coverage: 72.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAETDPKTVQDLTSVVQTLLQQMQDKFQTMSDQIIGRIDDMSSRIDDLEKNIADL
          .AETDPK.VQDLT..V...LQ....KFQTMSDQ.IG.IDDM...I.DLEKN..DL
Retrocopy VAETDPKIVQDLTLMVEMFLQHV*NKFQTMSDQTIGKIDDMNTLI-DLEKNVKDL

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	93.66 RPM
SRP007412_cerebellum	0.00 RPM	48.07 RPM
SRP007412_heart	0.03 RPM	45.23 RPM
SRP007412_kidney	0.03 RPM	115.25 RPM
SRP007412_liver	0.00 RPM	49.17 RPM
SRP007412_testis	0.00 RPM	193.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2288 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2288 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3367

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006485	3 retrocopies	retro_amel_20, retro_amel_261, retro_amel_646,
Canis familiaris	ENSCAFG00000019973	4 retrocopies	retro_cfam_1712, retro_cfam_395, retro_cfam_772, retro_cfam_874,
Callithrix jacchus	ENSCJAG00000000641	5 retrocopies	retro_cjac_1824, retro_cjac_2156, retro_cjac_3997, retro_cjac_708, retro_cjac_762,
Dasypus novemcinctus	ENSDNOG00000015303	3 retrocopies	retro_dnov_2535, retro_dnov_607, retro_dnov_7,
Equus caballus	ENSECAG00000026920	1 retrocopy	retro_ecab_580,
Homo sapiens	ENSG00000230989	2 retrocopies	retro_hsap_3076, retro_hsap_3367,
Latimeria chalumnae	ENSLACG00000022519	1 retrocopy	retro_lcha_96,
Loxodonta africana	ENSLAFG00000014112	2 retrocopies	retro_lafr_108, retro_lafr_15,
Macropus eugenii	ENSMEUG00000011483	2 retrocopies	retro_meug_1525, retro_meug_47,
Myotis lucifugus	ENSMLUG00000007636	1 retrocopy	retro_mluc_653,
Macaca mulatta	ENSMMUG00000020115	4 retrocopies	retro_mmul_169, retro_mmul_2120, retro_mmul_2184, retro_mmul_291,
Nomascus leucogenys	ENSNLEG00000026776	3 retrocopies	retro_nleu_1827, retro_nleu_2018, retro_nleu_963,
Otolemur garnettii	ENSOGAG00000015437	7 retrocopies	retro_ogar_1493, retro_ogar_2454, retro_ogar_2898, retro_ogar_488, retro_ogar_558, retro_ogar_796, retro_ogar_826,
Ochotona princeps	ENSOPRG00000005658	1 retrocopy	retro_opri_1092,
Procavia capensis	ENSPCAG00000004899	2 retrocopies	retro_pcap_322, retro_pcap_445,
Pan troglodytes	ENSPTRG00000008401	3 retrocopies	retro_ptro_2075, retro_ptro_2288 , retro_ptro_920,
Pteropus vampyrus	ENSPVAG00000006994	1 retrocopy	retro_pvam_1024,
Tupaia belangeri	ENSTBEG00000006478	1 retrocopy	retro_tbel_25,
Tarsius syrichta	ENSTSYG00000006648	7 retrocopies	retro_tsyr_1351, retro_tsyr_1428, retro_tsyr_1655, retro_tsyr_424, retro_tsyr_646, retro_tsyr_756, retro_tsyr_824,
Tursiops truncatus	ENSTTRG00000008666	3 retrocopies	retro_ttru_1618, retro_ttru_849, retro_ttru_866,