RetrogeneDB ID: retro_cfam_285

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:117807396..117808106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSCAFG00000013280
• Aliases: GLRX3, TXNL2
• Description: glutaredoxin 3 [Source:HGNC Symbol;Acc:15987]

Sequence

>retro_cfam_285
GTTCCCACTTTTCTGTTTTTCAAGAATTCTCAGAAAACTGACCGATTAGATGATGCACACACGCAAGAGTTGATCCAAAA
AGTTCAGGGACATGCATCTAGGTGGTTCCTTTCCACCTAGCGGTAGGAAGGATCCTAAAGATGTCAACCAAGCCTGAAGA
AATTCACCCAGGCTGCTCCCTGCAGGTTGTTCATGACAGGAACTCTTCAGGAACCATGTGGCGGGTTCAGCAAGCAGATG
GCAGACATTCTTAACGAACATAATTTTTGGTTTAGCAGATTTGATATCCTCTCAGGTGAAGAAGTTCATCAGGTCCTCAA
AACTTACTCCAATTGGCCCATCTATTCCCAGCTCTGTTCATGGAGAGCTCAGAGGAGGGCTTGACTGAATTAAGGATCCA
GAAACCTCTGAAGAACTAGATACAATTTGCCTCCACGCTCCCAAATTAGAGGAAAGATCCAAAGTACTGACAAATAAAGC
TTCTGTAATGAAATGTAATGAAAAACAACAGAAAGCAAAATGTGCATTCAGCTAACAAATTCCAGAAATACTAAATAGTA
CCAGTGTTGACTATGAGACATTTGATGATATATTAGAGAATAAGAATTTCGATAACAATTAAAAACTCAAATCGGCCAAC
ATACTCTCAGCTGTATGTGGAAGGGGAGCTTGTTGGATGAGTGCGTATCATTAAGAAACTGAAAGAAAAT

Alignment

ORF - retro_cfam_285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.38 %
• Parental protein coverage: 72.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VPTFLLFKNSQKIDRLDGAHAPELTKKVQRHAS-SGSFPPSTNEHPKEDLHVR-LKKLTHAAPCMLFMKG
          VPTFL.FKNSQK.DRLD.AH..EL..KVQ.HAS..GSF.P........D.....LKK.T.AAPC.LFM.G
Retrocopy VPTFLFFKNSQKTDRLDDAHTQELIQKVQGHAS>GGSF-PPSGRKDPKDVNQA<LKKFTQAAPCRLFMTG

Parental  TPQEPRCGFSKQMVEILNKHNIQFSSFDIFSDEEVRQGLKTYSNW-PTYPQLYVSGELIGGLDIIKELEA
          T.QEP..GFSKQM..ILN.HN..FS.FDI.S.EEV.Q.LKTYSNW.P..P...V.GEL.GGLD.IK..E.
Retrocopy TLQEPCGGFSKQMADILNEHNFWFSRFDILSGEEVHQVLKTYSNW>PSIPSS-VHGELRGGLD*IKDPET

Parental  SDELDTICPKAPKLEERLKVLTNKASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETF-DILEDE-EV
          S.ELDTIC..APKLEER.KVLTNKASVM.......Q.AKC.FS.QI.EILNST.V.YETF.DILE...E.
Retrocopy SEELDTICLHAPKLEERSKVLTNKASVMK-CNEKQQKAKCAFS*QIPEILNSTSVDYETFDDILENK<EF

Parental  RQGLKTYSNWPTYPQLYVKG-ELVGGLDIVKELKDN
          R..LKT.....T......KG.ELVG...I.K.LK.N
Retrocopy R*QLKTQIGQHTLSCMW-KG<ELVG*VRIIKKLKEN

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
SRP012049_cerebellum	0.04 RPM	56.87 RPM
SRP017611_brain	0.16 RPM	33.58 RPM
SRP017611_kidney	0.00 RPM	122.43 RPM
SRP017611_liver	0.00 RPM	25.23 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_285 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_285 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,