RetrogeneDB ID: retro_ptro_1917

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:116687694..116688026(-)
• Located in intron of: ENSPTRG00000030160

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHF5A
• Ensembl ID: ENSPTRG00000014427
• Aliases: None
• Description: PHD finger protein 5A [Source:HGNC Symbol;Acc:18000]

Sequence

>retro_ptro_1917
ATGGCTAAACATCATCCTGATTTGATGTTTTGCTGCAAGCAGACTGGTATTGCTATCGGAAGACTGTGTGAAAAATGTGA
TGGCAAGTGTGTGATTTGTGATTCCTATGTGCATCCCTGCACTCTGATGCACATATGTGATGAGCGTTAACTATGGATCT
TACCAGAGGTGCTGTGTGATCTGTGGAGGCCCTGGGGTTTCTGATGCCTATTATTGTAAGGAAGTGCACCATCCAGGAGA
AGGATAGGGATGGCTGCCCAAAGATTGTCAGTTTGGGTAACTCTAAGACAGACCTTTTCTATGAATGCAAAAAATACGGC
TTCAAGAAGAGG

Alignment

ORF - retro_ptro_1917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDE-CNYGSYQGRCVICGGPGVSDA
          MAKHHPDL.FC.KQ.G.AIGRLCEKCDGKCVICDSYV.PCTL..ICDE..NYGSYQ..CVICGGPGVSDA
Retrocopy MAKHHPDLMFCCKQTGIAIGRLCEKCDGKCVICDSYVHPCTLMHICDE>VNYGSYQRCCVICGGPGVSDA

Parental  YYCKE-CTIQEKDRDGCPKIVNLGSSKTDLFYERKKYGFKKR
          YYCKE.CTIQEKDRDGCPKIV.LG.SKTDLFYE.KKYGFKKR
Retrocopy YYCKE>CTIQEKDRDGCPKIVSLGNSKTDLFYECKKYGFKKR

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	0.20 RPM	7.54 RPM
SRP007412_cerebellum	0.57 RPM	3.30 RPM
SRP007412_heart	0.17 RPM	3.32 RPM
SRP007412_kidney	0.52 RPM	5.73 RPM
SRP007412_liver	0.39 RPM	5.70 RPM
SRP007412_testis	0.42 RPM	4.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1917 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1917 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2829

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015687	1 retrocopy	retro_amel_1674,
Canis familiaris	ENSCAFG00000001090	1 retrocopy	retro_cfam_369,
Callithrix jacchus	ENSCJAG00000004999	3 retrocopies	retro_cjac_1194, retro_cjac_1527, retro_cjac_906,
Echinops telfairi	ENSETEG00000010741	1 retrocopy	retro_etel_102,
Homo sapiens	ENSG00000100410	3 retrocopies	retro_hsap_2033, retro_hsap_2647, retro_hsap_2829,
Gorilla gorilla	ENSGGOG00000001104	2 retrocopies	retro_ggor_1848, retro_ggor_1965,
Latimeria chalumnae	ENSLACG00000012094	1 retrocopy	retro_lcha_25,
Microcebus murinus	ENSMICG00000013520	1 retrocopy	retro_mmur_758,
Macaca mulatta	ENSMMUG00000011354	3 retrocopies	retro_mmul_1390, retro_mmul_1471, retro_mmul_1503,
Mustela putorius furo	ENSMPUG00000016398	2 retrocopies	retro_mputfur_359, retro_mputfur_439,
Mus musculus	ENSMUSG00000061360	3 retrocopies	retro_mmus_1070, retro_mmus_1071, retro_mmus_1155,
Oryctolagus cuniculus	ENSOCUG00000012705	1 retrocopy	retro_ocun_640,
Otolemur garnettii	ENSOGAG00000002839	1 retrocopy	retro_ogar_55,
Pongo abelii	ENSPPYG00000011870	2 retrocopies	retro_pabe_1661, retro_pabe_2324,
Pan troglodytes	ENSPTRG00000014427	3 retrocopies	retro_ptro_1352, retro_ptro_1917 , retro_ptro_2479,
Pteropus vampyrus	ENSPVAG00000001162	1 retrocopy	retro_pvam_66,
Rattus norvegicus	ENSRNOG00000024170	3 retrocopies	retro_rnor_2660, retro_rnor_2704, retro_rnor_2712,
Tarsius syrichta	ENSTSYG00000001082	1 retrocopy	retro_tsyr_259,
Tursiops truncatus	ENSTTRG00000003369	1 retrocopy	retro_ttru_1483,