RetrogeneDB ID: retro_cfam_1886

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:67304341..67304957(-)
• Located in intron of: ENSCAFG00000018331

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNO1
• Ensembl ID: ENSCAFG00000003256
• Aliases: None
• Description: partner of NOB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:32790]

Sequence

>retro_cfam_1886
GACCCGACGGAGGCTCAGCCAGCCAAGAGGCCAATTTTCCCACTCCCCACTGGCCAGGGATTCCTGGGCGGGAAGGAAGA
AAGGAGGAAGATCCCAGGCCCAGCTAATAGACACATGCCATTCAAAGAGAACTGGACGAAGAGAGTTACTCCCATCCTAG
AACATTCGAGACTTCAGGTCCGCTTTACCTTGAAATTGAGGAATGTAGAAATCAGGACCTGTAAAGAAACGAAAGATGTC
TGTGCTCTGACAGAAGCAGTTAGTCCTGTGTAAGCCTTTCTTCTTGGGTTTCCAGTGGAGGAGGCACTTGCCCTCGTTAG
GTGGGATGACCTCTCTCTAGAGTCTCTTGAAATTACAGATGTGAAGCCTGTCAAGGGAGACCACCTGTCCAGGGCAATAG
GAAGAATCTCTGGCAAAGGAGAAACAACCAAATTTGCCATAAGAAAATGTGACACAGACACAGATAGTTTTGGCTGATGT
GAAAGTTCACAACGTTGGCTCTTTCTAAAGCATCAGGATGGCAAGAACTGCCATTTGCAACCTCATCCTGGGAAATCCTC
CATCACAGCTTTATGGCAGTATTCGAGCAGTGCTTAGCAGTGCAGCAGATCAGTTC

Alignment

ORF - retro_cfam_1886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.82 %
• Parental protein coverage: 80.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTEEARPAKRPVFPPLAGDGVLGGKEETRKIAVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVE
          D..EA.PAKRP.FP...G.G.LGGKEE.RKI..PANR..P.KENW.K..TPI.EH..LQ.RF.LK.RNVE
Retrocopy DPTEAQPAKRPIFPLPTGQGFLGGKEERRKIPGPANRHMPFKENWTKRVTPILEHSRLQVRFTLKLRNVE

Parental  IRTCKETKDVSALTKAADFVKAFILGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKG
          IRTCKETKDV.ALT.A...V.AF.LGF.VE.ALAL.R.DDL.LES.EITDVKP.KGDHLSRAIGRI.GKG
Retrocopy IRTCKETKDVCALTEAVSPV*AFLLGFPVEEALALVRWDDLSLESLEITDVKPVKGDHLSRAIGRISGKG

Parental  GKTKFTI-ENVTRTRIVLADVKVHILGSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRAADRF
          ..TKF.I.ENVT.T.IVLADVKVH..GSF..I.MARTAICNLILGNPPS..YG.IRAV.S.AAD.F
Retrocopy ETTKFAI>ENVTQTQIVLADVKVHNVGSF*SIRMARTAICNLILGNPPSQLYGSIRAVLSSAADQF

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	0.00 RPM	22.93 RPM
SRP017611_brain	0.00 RPM	17.63 RPM
SRP017611_kidney	0.00 RPM	34.54 RPM
SRP017611_liver	0.00 RPM	15.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1886 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886 ,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,