RetrogeneDB ID: retro_pabe_2830

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:4017639..4018524(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSPPYG00000002768
• Aliases: None
• Description: glutaredoxin 3 [Source:HGNC Symbol;Acc:15987]

Sequence

>retro_pabe_2830
CCTTGTGGTCCACAATGTGCACAGATGAACGAAGTTATGGCAGAATTAGCTAAAGAACGCCCTCAAGTTTCATTTGTGAA
GCTGGAAGCTGAAGGTGTTCCTGAAGTATCTGAAAAATATGAAATTAGCTCTGTTCCCACTTTTCTGTTTTTCAATAATT
CTCAGAAAATTGACCGACTAGATGGTGCACACATCCCAGAGTTGACCAAAAAAGTTCAGTGACATGCATCTACTGGCTCC
TTCCCACCCAGCACTAATGAACATCTTAAAGAAGATCGCAACCTTCGCTGAAAGAAATTGACTCATGCTGCCCCCTGCAT
GCCGTTTATGAAAGGAACTCCTCAAGAACCACTCTGTGGTTTCAGCAAGCAGTTGGTGGAAATTCGTCACAAACATAATA
TTTAGTTTAGCAGTTTTGATGCCTTCTCAGATGAAGACGTTCGACAGGGGCTCGAAGCCTATTCCAATTGGCCTACCTAT
CCTCAGCTCTACGTTTCTGGAGAGCTCATAGGAGGACTTGATATAATTAAGGAGCTACAAGCATCTGAAGAACTAGATAC
AATTTGTCCCAAAGCTCCCAAATTAGAGGAAAGGCTCAAAGTGCTGACAAATGAAGCTTCTGTGATGCTCTTTAAGAAAG
GAAACAAACAGGAAGCAAAATGTGGATTCAGCAAACAAATTCTGTAAATACTAAATAGTACTGGTGGTGAATATGAAATA
TTCGATATAGTGGAGGATGAAGGAGTTCGGCAAGGATTAAAAGCTTACTCAAACTGGCCAACATACCCTCAGCTGTATGT
GAAAGGGGAGCTGGTGGGAGGATTGGATATTGTGAAGGAGCTGAAAGAAAATGGTGAATTGCTGCCTATACTGAGGGGAG
AAAAT

Alignment

ORF - retro_pabe_2830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.85 %
• Parental protein coverage: 88.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PWAPQCAQMNEVMAELAKELPQVSFVKLEAEGVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTK
          P..PQCAQMNEVMAELAKE.PQVSFVKLEAEGVPEVSEKYEISSVPTFLFF.NSQKIDRLDGAH.PELTK
Retrocopy PCGPQCAQMNEVMAELAKERPQVSFVKLEAEGVPEVSEKYEISSVPTFLFFNNSQKIDRLDGAHIPELTK

Parental  KVQRHASSGSFLPSANEHLKEDLNLRLKKLTHAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFD
          KVQ.HAS.GSF.PS.NEHLKED.NLR.KKLTHAAPCM.FMKGTPQEP.CGFSKQ.VEI.HKHNI.FSSFD
Retrocopy KVQ*HASTGSFPPSTNEHLKEDRNLR*KKLTHAAPCMPFMKGTPQEPLCGFSKQLVEIRHKHNI*FSSFD

Parental  IFSDEEVRQGLKAYSNWPTYPQLYVSGELIGGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVML
          .FSDE.VRQGL.AYSNWPTYPQLYVSGELIGGLDIIKEL.ASEELDTICPKAPKLEERLKVLTN.ASVML
Retrocopy AFSDEDVRQGLEAYSNWPTYPQLYVSGELIGGLDIIKELQASEELDTICPKAPKLEERLKVLTNEASVML

Parental  FMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKE
          F.KGNKQEAKCGFSKQIL.ILNSTG.EYE.FDI.EDE.VRQGLKAYSNWPTYPQLYVKGELVGGLDIVKE
Retrocopy FKKGNKQEAKCGFSKQIL*ILNSTGGEYEIFDIVEDEGVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKE

Parental  LKENGELLPILRGEN
          LKENGELLPILRGEN
Retrocopy LKENGELLPILRGEN

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	0.06 RPM	14.76 RPM
SRP007412_cerebellum	0.24 RPM	19.21 RPM
SRP007412_heart	0.06 RPM	14.69 RPM
SRP007412_kidney	0.03 RPM	17.67 RPM
SRP007412_liver	0.03 RPM	20.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2830 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2830 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830 ,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,