RetrogeneDB ID: retro_cfam_1490

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:5163882..5164534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSCAFG00000017383
• Aliases: LOC608758, APOOL
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_cfam_1490
ATAGCAGCTGTTAGGATGGGAAAGCTGATAACCATACCTGCAGGTCTGATATGTGCATCTATAACTGTGCATGCGGCTAA
AGAAGAAGAATACAAAAAGCAGCTAGTGAAACCAGAATGGCTTCCCGTATAAACTGCATCACCTCTGCAATCTAAATATG
TTGAGGAACAGCCTGGTCATTTACAAATGGGCTTTGCATCCATTTGCACTACAACTGGTCATTATATTGGCTGATGCAAG
AGTGTTTATGTGTTTGTGAAAAATGGAATAATGGATACAGTACAATCTGGAAAAGATGCATATGTCTATCTGAAGAATCC
ACCTTGAGATTTTCTTCCAAAAGTTGGAGCGATTACTCTTTCAGGATTGATAGGCTTGGTTTTGGCAAGAAAAGGTTCTA
GGTTTAAGAAAATTGCTTATCCACTGGGACTGGCCACTTTGGGAGCAGCTGTTTGCTAACCAGTTCAGTCAGTAATAATT
GCAAAGGTAACTGGGAAAAAGACATACACTACAAGCGAGCAAATTTATGAAGCAGTTAAATCATTGTGGACAAACATACA
AAAAATAGTCCTTTCCTAAGTCTAAAGAAAAATCCAAGCTAGGGAATTCTGCTGAAATAGAAATACCTGCAAAAACAACT
CACAGCCTAGAA

Alignment

ORF - retro_cfam_1490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 81.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAVRMGKLTTVPAGLICASITVHAAKEE-YKKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRT
          .AAVRMGKL.T.PAGLICASITVHAAKEE.YKKQLVKPE.LP..TA.PLQSKYVEEQPGHLQMGFASI.T
Retrocopy IAAVRMGKLITIPAGLICASITVHAAKEEEYKKQLVKPEWLPV*TASPLQSKYVEEQPGHLQMGFASICT

Parental  TTSHYIGWCKGVYVFMKNGIMDTVQFGKDVYVYLKNPPRDFLPKIGVITVSGLAGLVSARKGSRFKKIAY
          TT.HYIG.CK.VYVF.KNGIMDTVQ.GKD.YVYLKNPP.DFLPK.G.IT.SGL.GLV.ARKGSRFKKIAY
Retrocopy TTGHYIG*CKSVYVFVKNGIMDTVQSGKDAYVYLKNPP*DFLPKVGAITLSGLIGLVLARKGSRFKKIAY

Parental  PLGLATLGAAVCYPVQSVIIAKVTGKKAYTASEQIYEAVKSLWTKI-NKKESFPKPKEKP-KLGNSAEIE
          PLGLATLGAAVC.PVQSVIIAKVTGKK.YT.SEQIYEAVKSLWT.I..K...F...K..P.KLGNSAEIE
Retrocopy PLGLATLGAAVC*PVQSVIIAKVTGKKTYTTSEQIYEAVKSLWTNI<TKNSPFLSLKKNP<KLGNSAEIE

Parental  IPAKTADSLK
          IPAKT..SL.
Retrocopy IPAKTTHSLE

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	3.28 RPM
SRP017611_brain	0.00 RPM	2.06 RPM
SRP017611_kidney	0.00 RPM	32.56 RPM
SRP017611_liver	0.00 RPM	13.71 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1490 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1490 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490 ,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,