RetrogeneDB ID: retro_ptro_2320

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:3978430..3979035(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSPTRG00000003060
• Aliases: GLRX3, TXNL2
• Description: None

Sequence

>retro_ptro_2320
GATCTCAACCTTCGCTTACAGAAACTGACTCATGCTGCCCCCTGCATGCTGTTTATGAAAAGGAACTCCTCAAGAACCAC
TCTGTGGTTTCAGCAAGCAGATGGTGGAAATTCTTCACAAACATAATATTTAGTTTAGCAGTTTTGATGTCTTCTGAGAT
CAAGAGGTTCGACAGGGGCTCAAAGCCTATTCCAATTGGCCTACCTATCCTCAGCTCTACGTTTCTGGAGAGCTCATAGG
AGGACTTGATATAATTAAGGAGCTACACGCATCTGAAGAACTAGATACAATTTGTCCCAAAGCTCCCAAATTAGAGGAAA
GGCTCAAAGTGCTGACAAATGAAGCTTCTATGATGCTCTTTATGAAACAAACAGAAAGCAAAATGTGGATTCAGGAAACA
AATTCTGGAAATACTAAATAGTACTGGTGGTGAATATGAAACATTCGATATACTGGATGAAGGAGTTCGGCAAGGATTAA
AAGATTACTCAAATTGGCCAACATATCCTCAGCTGTATGTGAAAGGGGAGCTGGTGGGAGGATTGGATATTGTGAAGGAG
CTGAAAGACAATGGTGAATTGCTGCCTATACTGAGAGGAGAAAAT

Alignment

ORF - retro_ptro_2320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.83 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLNLRLKKLTHAAPCMLFMK-GTPQEPRCGFSKQMVEILHKHNVQFSSFDIFSDEEVRQGLKAYSNWPTY
          DLNLRL.KLTHAAPCMLFMK.GTPQEP.CGFSKQMVEILHKHN..FSSFD.F.D.EVRQGLKAYSNWPTY
Retrocopy DLNLRLQKLTHAAPCMLFMK>GTPQEPLCGFSKQMVEILHKHNI*FSSFDVF*DQEVRQGLKAYSNWPTY

Parental  PQLYVSGELIGGLDIIKELEASEELDTICPKAPKLEERLKVLTNKASVMLFMKGNKQEAK-CGFSKQILE
          PQLYVSGELIGGLDIIKEL.ASEELDTICPKAPKLEERLKVLTN.AS.MLFMK....E.K.CGF.KQILE
Retrocopy PQLYVSGELIGGLDIIKELHASEELDTICPKAPKLEERLKVLTNEASMMLFMK--QTESK>CGFRKQILE

Parental  ILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQLYVKGELVGGLDIVKELKENGELLPILRGEN
          ILNSTG.EYETFDIL.DE.VRQGLK.YSNWPTYPQLYVKGELVGGLDIVKELK.NGELLPILRGEN
Retrocopy ILNSTGGEYETFDIL-DEGVRQGLKDYSNWPTYPQLYVKGELVGGLDIVKELKDNGELLPILRGEN

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	21.06 RPM
SRP007412_cerebellum	0.00 RPM	17.57 RPM
SRP007412_heart	0.00 RPM	24.34 RPM
SRP007412_kidney	0.00 RPM	25.68 RPM
SRP007412_liver	0.00 RPM	30.61 RPM
SRP007412_testis	0.11 RPM	96.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2320 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2320 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2308

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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 ,