RetrogeneDB ID: retro_pabe_2986

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:110844094..110844957(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF259
• Ensembl ID: ENSPPYG00000025914
• Aliases: None
• Description: zinc finger protein 259 [Source:HGNC Symbol;Acc:13051]

Sequence

>retro_pabe_2986
ATGGCGGCCACCGGGGCTGTGGAAGTGGGGTCCCCGGGGTCAGCCATTGCCCCCTCGCCCACCCTGGCCTTGCTGCCCAC
CCTGAGTCATCTGTTCCGGCCCATCAGCACCGAGGACGAGGAGCAGCAGCCCACCCAGATCAAGTCGCTGTGCATAAACT
GTTACCGCAATGGCATGACGCGCCTCCTGCTCACCAAGATTCCCTTCTTCAGAGAAATAATCGTGAGCTCCTTTTCCTGC
CACCACTGTGGCTGGAACAACATGGAGATCCAATCAGCAGGCAGGATCCAGGACCAGGGAGTGTGCTACACTTTGAGCCT
CAGGGCTCTGGAGGACATGAACAGAGAAGTGGTGAAGACTGACTCTGCTACCACAGGGATTCCTGAGCTAGATTTTCAAA
TTCCTGCCTTTAGCCAGAAAGGAGCTCTGAACACTGTTGAAGGATTGATCACCCATGCTATCTCTGGCCTGAAGCAGGAC
TAGCCTGCATGAAGGGCAACAAAGATGCCACAGCTGAAAGAGTTGATGAGTTCATTGTCAAACTGAAGGAGCTAAAGCAA
GCAGCCTCCCCTTTCACTCTGATCATTGACGATCCCTCAGGAAACAGCTTTGTGGAAAACCCATATGCTGCTCAGAAAGA
TGATGCCCTGGTGATCACACACCACAACCGGACCCGGCAGCAGGAAGAGATGCTGGGGCTCCAAGCAGAAGCACCAACAG
AGAAGCCAGAAGAGGAAGATCTCAGAAATGAAGTGCTCCAGTTTAACACAAACGGCCCAAAATGCAATGCCCCCGCTCAG
ACCAACATGAAGTTAGTACAAATCCTTCACTTTAAGGAGGGACCAACTGCAAGAACTGCGTGT

Alignment

ORF - retro_pabe_2986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.39 %
• Parental protein coverage: 62.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASGAVEPGPPGAAVAPSPAPTPPPAPDHLFRPISAEDEEQQPTEIESLCMNCYCNGMTRLLLTKIPFF
          MAA.GAVE.G.PG.A.APSP.....P...HLFRPIS.EDEEQQPT.I.SLC.NCY.NGMTRLLLTKIPFF
Retrocopy MAATGAVEVGSPGSAIAPSPTLALLPTLSHLFRPISTEDEEQQPTQIKSLCINCYRNGMTRLLLTKIPFF

Parental  REIIVSSFSCEHCGWNNTEIQSAGRIQDQGVRYTLSVRALEDMNREVVKTDSAATRIPELDFEIPAFSQK
          REIIVSSFSC.HCGWNN.EIQSAGRIQDQGV.YTLS.RALEDMNREVVKTDSA.T.IPELDF.IPAFSQK
Retrocopy REIIVSSFSCHHCGWNNMEIQSAGRIQDQGVCYTLSLRALEDMNREVVKTDSATTGIPELDFQIPAFSQK

Parental  GALTTVEGLITRAISGLEQDQPARRA-NKDATAERIDEFIVKLKELKQVASPFTLIIDDPSGNSFVENPH
          GAL.TVEGLIT.AISGL.QD.PA.RA.NKDATAER.DEFIVKLKELKQ.ASPFTLIIDDPSGNSFVENP.
Retrocopy GALNTVEGLITHAISGLKQD*PA*RA<NKDATAERVDEFIVKLKELKQAASPFTLIIDDPSGNSFVENPY

Parental  APQKDDALVITHYNRTRQQEEMLGRQEEAPAEKPEEEDLRNEVLQFNTNCPECNAPAQTNMKLVQIPHFK
          A.QKDDALVITH.NRTRQQEEMLG.Q.EAP.EKPEEEDLRNEVLQFNTN.P.CNAPAQTNMKLVQI.HFK
Retrocopy AAQKDDALVITHHNRTRQQEEMLGLQAEAPTEKPEEEDLRNEVLQFNTNGPKCNAPAQTNMKLVQILHFK

Parental  EVIIMATNC
          E.....T.C
Retrocopy EGPTARTAC

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	2.76 RPM	14.87 RPM
SRP007412_cerebellum	1.95 RPM	9.61 RPM
SRP007412_heart	0.87 RPM	5.27 RPM
SRP007412_kidney	2.06 RPM	11.34 RPM
SRP007412_liver	1.53 RPM	12.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2986 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2986 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3639
Pan troglodytes	retro_ptro_2464
Gorilla gorilla	retro_ggor_2455

---

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,