RetrogeneDB ID: retro_ptro_562

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:84367983..84368452(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSPTRG00000000467
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_ptro_562
ATGAATCACCCAGCTCCAGTGGAAGTCACATACGGGAACATGAGATTTCTTATTATACACAACCCAACCAATTCGACCTT
AAACAGATTTTTAGAAGAACTTAAGAAATAGGGGGTTACCACAATAGTAAGAGTATGTGAAGCAACTGATGACCCTGCTC
TTGTGGAGAAAGAAGGCCAATCCAGTTTCTGGATTGGCCTTTTGATGATGGTTCATCACCATCCAACCAGATTGTTGATC
ACTGGTTAAGTCTTCTAGACGTTAAGTTTCGTGAAGAACCTGGTTGTTGTATTGCCTTCACTGTGTTGCAGGTCTTGGGA
GGACTCCAGTGCTTGTTGCCCTAGCATTAATTGAAAGTGGAATGAAAAACGAAGATGCAGTACGGTTTATTAGAGATAAA
TGGCACGGCGCTTTTAACAGCAAGCAACTTTTGTATTTGGAGAAATATCATTCTCAAATGCGGCTTCGC

Alignment

ORF - retro_ptro_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.21 %
• Parental protein coverage: 93.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLFRVCDATYEKAPVE-KEGNHV-LDWPFD
          MN.PAPVE..Y.NMRFLI.HNPTN.TLN.F.EELKK.GVTT..RVC.AT...A.VE.K..N.V.LDWPFD
Retrocopy MNHPAPVEVTYGNMRFLIIHNPTNSTLNRFLEELKK*GVTTIVRVCEATDDPALVE>KKANPV>LDWPFD

Parental  DGAPPPNQIVDDWLNLLKTKFREEPGCCVA-VHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGA
          DG..P.NQIVD.WL.LL..KFREEPGCC.A..HCVAGLGR.PVLVALALIE.GMK.EDAV.FIR.K..GA
Retrocopy DGSSPSNQIVDHWLSLLDVKFREEPGCCIA<LHCVAGLGRTPVLVALALIESGMKNEDAVRFIRDKWHGA

Parental  FNSKQLLYLEKYRPKMRLR
          FNSKQLLYLEKY...MRLR
Retrocopy FNSKQLLYLEKYHSQMRLR

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	0.02 RPM	48.49 RPM
SRP007412_cerebellum	0.00 RPM	29.93 RPM
SRP007412_heart	0.03 RPM	84.15 RPM
SRP007412_kidney	0.00 RPM	45.84 RPM
SRP007412_liver	0.00 RPM	32.21 RPM
SRP007412_testis	0.00 RPM	82.62 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_562 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_562 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_807
Gorilla gorilla	retro_ggor_662
Pongo abelii	retro_pabe_721
Callithrix jacchus	retro_cjac_910
Mus musculus	retro_mmus_3053
Rattus norvegicus	retro_rnor_612
Oryctolagus cuniculus	retro_ocun_225
Bos taurus	retro_btau_1186
Canis familiaris	retro_cfam_206
Equus caballus	retro_ecab_20

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017806	1 retrocopy	retro_amel_1484,
Choloepus hoffmanni	ENSCHOG00000010834	1 retrocopy	retro_chof_2029,
Macropus eugenii	ENSMEUG00000002037	1 retrocopy	retro_meug_2,
Microcebus murinus	ENSMICG00000001424	5 retrocopies	retro_mmur_1393, retro_mmur_1475, retro_mmur_338, retro_mmur_822, retro_mmur_910,
Macaca mulatta	ENSMMUG00000012930	1 retrocopy	retro_mmul_1235,
Pan troglodytes	ENSPTRG00000000467	4 retrocopies	retro_ptro_1212, retro_ptro_562 , retro_ptro_654, retro_ptro_727,
Pan troglodytes	ENSPTRG00000018314	4 retrocopies	retro_ptro_1657, retro_ptro_2239, retro_ptro_3190, retro_ptro_360,