RetrogeneDB ID: retro_pabe_317

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:166044897..166045636(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSPPYG00000008402
• Aliases: None
• Description: dnaJ homolog subfamily C member 7 [Source:RefSeq peptide;Acc:NP_001126143]

Sequence

>retro_pabe_317
CATGAGAGGGTCTGCGTTGCTTGTAGAAATCCCAAAGCACTCAAAGCAAAGAAAGAAGACAGAAATAAAGCATTTAAGGA
AGGAAATTACAAGCTAGCATACGAACTGTACACATGAGCCCTGGGGATAAACCCCAACAATATAAAAATACATGCTAAAC
TCTACTATAATCAAGTTATGGTTAATTCTAAGCTTAGGAAACTGGTTATGCAATACAAGACTGCAAAAATACAGTGAAGC
TCAATGACACCTATTTAAAAGCCTGCTTGAGAAGAGCTCAGTGTTACATGAACACCAAACAGTATGAAGAAGCAGTGCAC
AATTATGAAAAAGTGTATCAGACAGAGAAAACAAAAGAACACAAACAGCTCCTAAAAAATGCACAGCTGAAACTGAAGAA
GAGTAAGAAGAAAGATTACTACAAGATTCTGGGAATGGACAATAATGCCTCTGAGGACGAGACCAAGAAAGTTCATCACA
AATGGGCCCTGATGGACCATCCAGATTGGCACAGTGGAGGCAGTGCTGAGGTTCAGAAGGAGGAGGGGAAGTTCAAGGAA
ATTGGAGAGGCCTTTACCATCTTCTCTGATCCCAAGAAAAAGACTTGCTAGGACAGTGGACAGGACCTGGACAAGGAGGG
CATGAATATGGGTGATTTTGATGCAAATAGTATCTTCAAGGCATTCTTCAGTGGTCTTGGGGCTTCAGCTTTGAAGCATC
TGGTCCAGGGAATTTTTTT

Alignment

ORF - retro_pabe_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 50.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEALGIDPNNIKTNAKLYCNRGTVNSKLRKL-D
          HE..C.ACRN.KALKAKKED.NKAFKEGNYKLAYELYT.ALGI.PNNIK..AKLY.N...VNSKLRKL..
Retrocopy HERVCVACRNPKALKAKKEDRNKAFKEGNYKLAYELYT*ALGINPNNIKIHAKLYYNQVMVNSKLRKL<G

Parental  DAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLELKKSKRKD
          .AI.DC.N.VKL.DTY.KA.LRRAQCYM.T.QYEEAV..YEKVYQTEKTKEHKQLLKNAQL.LKKSK.KD
Retrocopy YAIQDCKNTVKLNDTYLKACLRRAQCYMNTKQYEEAVHNYEKVYQTEKTKEHKQLLKNAQLKLKKSKKKD

Parental  YYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQKEEEKKFKEVGEAFTILSDPKKKTRYDSGQ
          YYKILG.D.NASEDE.KK...K.ALM.HPD.HSG.SAEVQK.EE.KFKE.GEAFTI.SDPKKKT..DSGQ
Retrocopy YYKILGMDNNASEDETKKVHHKWALMDHPDWHSGGSAEVQK-EEGKFKEIGEAFTIFSDPKKKTC*DSGQ

Parental  DLDEEGMNMGDFDPNNIFKAFFGGPG-GFSFEASGPGNFF
          DLD.EGMNMGDFD.N.IFKAFF.G.G.GFSFEASGPGNFF
Retrocopy DLDKEGMNMGDFDANSIFKAFFSGLG<GFSFEASGPGNFF

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	72.04 RPM
SRP007412_cerebellum	0.00 RPM	61.89 RPM
SRP007412_heart	0.00 RPM	16.44 RPM
SRP007412_kidney	0.00 RPM	43.65 RPM
SRP007412_liver	0.00 RPM	23.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_317 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_317 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_398
Pan troglodytes	retro_ptro_304
Macaca mulatta	retro_mmul_501

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317 ,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,