RetrogeneDB ID: retro_cfam_289

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:10598126..10598753(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000048
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTOV1
• Ensembl ID: ENSCAFG00000003495
• Aliases: None
• Description: prostate tumor overexpressed 1 [Source:HGNC Symbol;Acc:9632]

Sequence

>retro_cfam_289
CTGATGGGCAACGGCTTCGCGGGGTGTGTGCTCTTTCCCCACATCTCCCCTGCGAGGTGCGCTACTCATGCTCCTGTACT
CGTCCAAGAAGATCTTCACGGGCCTCATCCCCTACGACCAGAGCGGTTTCCTCAAGGCCATCCGGCAGGTCATCACCACG
CGCAAACAGGCAGTGGGCCCTGGTGGTGTCGGGGGCCGGGCCCAGATCGTCAACAACAAGCTCCTAGCGTGGAGTGGAGT
CATGGAGTGGCAGGAGCCCAGGCCTGAGCCCAACAGTGGGTCCAAGAGGTGGCTGCCATCGCATGTCTACGTGAACCCAG
GGGAGATCCTGAGGACTGAGCAGTGGCCAAGGAAGCTGTACATGCAGCTCATCCCACAGCAGCTGCTGACCACCTGGTAC
CACAGTTTTGGAACTCGCGCCTGGTCCAGTTCCACTTCACCAAGGACCTGGAGACGCTGAACAGCCTGTGCCGGATGGTG
GACAATGGCTTTGCCAGCTGCGTGCACTTTTCCTACAAGGCATCGTGCAAGGTGCGCGTGCTCATGCTCCTGTACTCGTC
GGAGAAGAAGATCTTCATTGGCCTCATCCCCCATGACCAGAGCAACTTCGTCAACGGCATCCGGCGG

Alignment

ORF - retro_cfam_289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.25 %
• Parental protein coverage: 50.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VMGNGFAGCMLFPHISP-CEVR-VLMLLYSSKKKIFMGLIPYDQSGFVNAIRQVITTRKQAVGPGGVAGP
          .MGNGFAGC.LFPHISP.CEVR..LMLLYSSKK.IF.GLIPYDQSGF..AIRQVITTRKQAVGPGGV.G.
Retrocopy LMGNGFAGCVLFPHISP<CEVR<LLMLLYSSKK-IFTGLIPYDQSGFLKAIRQVITTRKQAVGPGGVGGR

Parental  VQIVNNKFLAWSGVMEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTT-LVPL
          .QIVNNK.LAWSGVMEWQEPRPEPNS.SKRWLPSHVYVN.GEILRTEQWPRKLYMQLIPQQLLTT.LVP.
Retrocopy AQIVNNKLLAWSGVMEWQEPRPEPNSGSKRWLPSHVYVNPGEILRTEQWPRKLYMQLIPQQLLTT<LVPQ

Parental  FRNSRLVQFHFTKDLETLKSLCRIMDNGFAGCVHFSYKASCEVRVLMLLYSSEKKIFIGLIPHDQSNFVN
          F.NSRLVQFHFTKDLETL.SLCR..DNGFA.CVHFSYKASC.VRVLMLLYSSEKKIFIGLIPHDQSNFVN
Retrocopy FWNSRLVQFHFTKDLETLNSLCRMVDNGFASCVHFSYKASCKVRVLMLLYSSEKKIFIGLIPHDQSNFVN

Parental  GIRR
          GIRR
Retrocopy GIRR

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	215.12 RPM
SRP017611_brain	0.00 RPM	88.13 RPM
SRP017611_kidney	0.00 RPM	53.16 RPM
SRP017611_liver	0.00 RPM	35.39 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_289 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289 ,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818,