RetrogeneDB ID: retro_cfam_2153

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:43957032..43957434(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPV
• Ensembl ID: ENSCAFG00000018019
• Aliases: None
• Description: centromere protein V [Source:HGNC Symbol;Acc:29920]

Sequence

>retro_cfam_2153
GGCGCGCAGCGGTAGCGCCGGGAGACGTTCAGGAAGCGGCGGGGCCTCATCGGCGAGGGCGCCGCCAAGTTCCTGCTGGA
CACCTTCGAGTACCCCGGCCTGGTGTATCGCACCGGCGGCTGCCACTGCGGCGCGGTCCGCTTCGCGGTCTGGGCGCCCG
CAGACCTGCGCATGGTGGATTGCAGCTGCAGGCTGTGCAGGAAGAAGCAGCATCGACACTTCCTCGTCCCGGCCTCGCGC
TTCACTCTGCTGCTGGGCGCCTAGAGCATCCTCACGTATCGGTCCCACACGCACCCGGCGCTGCACAGCTTCTGCAGCAG
GTGCGGCGTGCAGAGTTTCCACGCATCTGTCTCTGACCCCGGCATTTACGGCGTCGCCCCGCACTGCCTGGACAAGGAAA
CA

Alignment

ORF - retro_cfam_2153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.16 %
• Parental protein coverage: 78.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQQRERWETFQKRQRLTFEGAAKLLLDTFEYQGLVKHTGGCHCGAVRFEVWASADLHIFDCNCSICKKKQ
          G.QR.R.ETF.KR..L..EGAAK.LLDTFEY.GLV..TGGCHCGAVRF.VWA.ADL...DC.C..C.KKQ
Retrocopy GAQR*RRETFRKRRGLIGEGAAKFLLDTFEYPGLVYRTGGCHCGAVRFAVWAPADLRMVDCSCRLCRKKQ

Parental  NRHFIVPASRFKLLKGAESITTYTFNTHKAQHTFCKRCGVQSFYTPRSNPGGFGIAPHCLDEGT
          .RHF.VPASRF.LL.GA.SI.TY...TH.A.H.FC.RCGVQSF....S.PG..G.APHCLD..T
Retrocopy HRHFLVPASRFTLLLGA*SILTYRSHTHPALHSFCSRCGVQSFHASVSDPGIYGVAPHCLDKET

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	19.32 RPM
SRP017611_brain	0.00 RPM	4.37 RPM
SRP017611_kidney	0.00 RPM	4.03 RPM
SRP017611_liver	0.00 RPM	2.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2153 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004716	5 retrocopies	retro_amel_1859, retro_amel_1870, retro_amel_1909, retro_amel_1926, retro_amel_924,
Canis familiaris	ENSCAFG00000018019	2 retrocopies	retro_cfam_2153 , retro_cfam_2155,
Homo sapiens	ENSG00000166582	3 retrocopies	retro_hsap_4683, retro_hsap_4833, retro_hsap_4834,
Macropus eugenii	ENSMEUG00000002027	1 retrocopy	retro_meug_519,
Microcebus murinus	ENSMICG00000007166	1 retrocopy	retro_mmur_1491,
Mustela putorius furo	ENSMPUG00000010146	2 retrocopies	retro_mputfur_1195, retro_mputfur_39,
Nomascus leucogenys	ENSNLEG00000014726	1 retrocopy	retro_nleu_2709,
Otolemur garnettii	ENSOGAG00000029365	1 retrocopy	retro_ogar_99,
Pan troglodytes	ENSPTRG00000008810	1 retrocopy	retro_ptro_3216,
Ictidomys tridecemlineatus	ENSSTOG00000012221	2 retrocopies	retro_itri_110, retro_itri_1540,