RetrogeneDB ID: retro_ptro_2464

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:109846545..109847408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF259
• Ensembl ID: ENSPTRG00000004312
• Aliases: None
• Description: None

Sequence

>retro_ptro_2464
ATGGCGGCCACCGGGGCTGTGGAAGTGGGGTCCCCGGGGTCAGCCGTTGCCCCCTCGCCCGCCCTGGACTTGCTGCCTGC
CCTGGGTCATCTGTTCTGGCCCATCAGCGCCGAGGACAAGGAGCAGCAGCCCACCCAGATCAAGTCACTGTGCATGAACT
GTTACCGCAATGGCATGACGCGCCTCCTGCTCACCAAGATTCCCTTCTTCAGAGAAATAATCGTGAGCTCCTTTTCCTAC
CACCACTGTGGCTGGAACAACATGGAGATCCAATCGGCAGGCAGGATCCAGGACCAGGGAGCGCGCTACACTTTGAGCAT
CAGGGCTCTGGAGGACATGAACAGAGAAGTGGTGAAGACTGACTCCGCTACCACAAGGATTCCTGAGCTAGATTTTCAAA
TTCCTGCCTTTAGCCAGAAAGGAGCTCTGAACACTGTTGAAGGATTGATCACCCGTGCTATCTCTGGCCGGGAGCAGGAC
TAGCCTGCGCGAAGGGCAACAAAGATGCCACAGCTGAAAGAATTGATGAGTTCATTGTCAAACTGAAGGAGCTAAAGCAA
TCAGCCTCCCCTTTCACTCTGATCATTGATGATCCCTGAGGGAACAGCTTTGTGGAAAACCCACATGCTGCTCAGAAAGA
TGATGCCCTGGTGATCACACACTACAACCAGACCCGACAGCAGGAAGAGATGCTGGGGCTCCAAGCAGAAGCACCAACAG
AGAAGCCAGAAGAGGAAGATCTCAGAAATGAAGTGCTCCAGTTTAACACAAACGGCCCAGAATGCAATGCCCCTACTCAG
ACCAATATGAAGCTAGTACAAATCCCTCACTTTAAGGAGGGACCAACTACAAGAACTGCGTGC

Alignment

ORF - retro_ptro_2464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.81 %
• Parental protein coverage: 62.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASGAVEPGPPGAAVAPSPAPAPPPAPDHLFRPISAEDEEQQPTEIESLCMNCYCNGMTRLLLTKIPFF
          MAA.GAVE.G.PG.AVAPSPA....PA..HLF.PISAED.EQQPT.I.SLCMNCY.NGMTRLLLTKIPFF
Retrocopy MAATGAVEVGSPGSAVAPSPALDLLPALGHLFWPISAEDKEQQPTQIKSLCMNCYRNGMTRLLLTKIPFF

Parental  REIIVSSFSCEHCGWNNTEIQSAGRIQDQGVRYTLSVRALEDMNREVVKTDSAATRIPELDFEIPAFSQK
          REIIVSSFS..HCGWNN.EIQSAGRIQDQG.RYTLS.RALEDMNREVVKTDSA.TRIPELDF.IPAFSQK
Retrocopy REIIVSSFSYHHCGWNNMEIQSAGRIQDQGARYTLSIRALEDMNREVVKTDSATTRIPELDFQIPAFSQK

Parental  GALTTVEGLITRAISGLEQDQPARRA-NKDATAERIDEFIVKLKELKQVASPFTLIIDDPSGNSFVENPH
          GAL.TVEGLITRAISG.EQD.PARRA.NKDATAERIDEFIVKLKELKQ.ASPFTLIIDDP.GNSFVENPH
Retrocopy GALNTVEGLITRAISGREQD*PARRA<NKDATAERIDEFIVKLKELKQSASPFTLIIDDP*GNSFVENPH

Parental  APQKDDALVITYYNRTRQQEEMLGLQEEAPAEKPEEEDLRNEVLQFNTNCPECNAPAQTNMKLVQIPHFK
          A.QKDDALVIT.YN.TRQQEEMLGLQ.EAP.EKPEEEDLRNEVLQFNTN.PECNAP.QTNMKLVQIPHFK
Retrocopy AAQKDDALVITHYNQTRQQEEMLGLQAEAPTEKPEEEDLRNEVLQFNTNGPECNAPTQTNMKLVQIPHFK

Parental  EVIIMATNC
          E.....T.C
Retrocopy EGPTTRTAC

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	19.80 RPM
SRP007412_cerebellum	0.07 RPM	18.78 RPM
SRP007412_heart	0.03 RPM	10.08 RPM
SRP007412_kidney	0.05 RPM	22.62 RPM
SRP007412_liver	0.03 RPM	31.49 RPM
SRP007412_testis	0.00 RPM	99.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2464 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2464 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3639
Gorilla gorilla	retro_ggor_2455
Pongo abelii	retro_pabe_2986

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011907	1 retrocopy	retro_etel_246,
Homo sapiens	ENSG00000109917	1 retrocopy	retro_hsap_3639,
Gorilla gorilla	ENSGGOG00000000664	1 retrocopy	retro_ggor_2455,
Myotis lucifugus	ENSMLUG00000014012	1 retrocopy	retro_mluc_2167,
Macaca mulatta	ENSMMUG00000020287	1 retrocopy	retro_mmul_1808,
Mus musculus	ENSMUSG00000032078	2 retrocopies	retro_mmus_3602, retro_mmus_3701,
Otolemur garnettii	ENSOGAG00000009977	1 retrocopy	retro_ogar_506,
Pongo abelii	ENSPPYG00000025914	1 retrocopy	retro_pabe_2986,
Pan troglodytes	ENSPTRG00000004312	1 retrocopy	retro_ptro_2464 ,
Sus scrofa	ENSSSCG00000015066	1 retrocopy	retro_sscr_1150,