RetrogeneDB ID: retro_cfam_807

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:39640681..39641300(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS72
• Ensembl ID: ENSCAFG00000012540
• Aliases: None
• Description: vacuolar protein sorting 72 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:11644]

Sequence

>retro_cfam_807
CTGCCACTAGAACTACAGGACGATGGCTCCGACAGCAGAAGTCCATGCGTCAATCTACAGCTGAGCATACACGACAGACA
TTCCTTCGGGTACAAGAGAGGCAGGGCCAGTCACAGTCGGCAAAAGGGGCCCCATTGTGAGCGGCCTCTGACCCAGCAAG
AGCTGCTCAGAGAGGCCAAGATCACAGAAGAGCTCAACTTACGTTCACTGGAGACATACGAGAGGCTCGAGGCTGACAAA
AAGAAGCAGGTGCACAAGAAGAGGAAGTGCCCTGGGCCCATAATCACCTATCATTCGGTTACAGTGCCCCTTGTTGGGGA
GCCAGGCCCTAAAGAAGAGAATGTGGATGTGGAAGGGCTGGATCCTACTCCCACAGCTTCTGCACTGACTCCCCATGCCG
GCACTGGACCGGTTGTCTCTCCACCTCGCTGCTTGCATACTTTCATCATTTTTAGTGATGATGCAACATTTGAGGAATGG
TTTTCCCCAAGGCCGGCCCCCAAAGGTCCCTGTTCGGGAGGTCTGCCCCGTGACCCATCGCCCAGCCCTGTACCGGGACC
CTGTCACAGACATCCCCTACACCACTGCTCGAGCCTTCAAGATCATCCGTGAGGCCTAC

Alignment

ORF - retro_cfam_807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 55.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LPLELQDDGSDSR-KSMRQSTAEHTRQTFLRVQERQGQSR-RRKGPHCERPLTQEELLREAKITEELNLR
          LPLELQDDGSDSR.KSMRQSTAEHTRQTFLRVQERQGQS..R.KGPHCERPLTQ.ELLREAKITEELNLR
Retrocopy LPLELQDDGSDSR<KSMRQSTAEHTRQTFLRVQERQGQSQ>RQKGPHCERPLTQQELLREAKITEELNLR

Parental  SLETYERLEADKKKQVHKKRKCPGPIITYHSVTVPLVGEPGPKEENVDVEGLDPTPTASALTPHAGTGPV
          SLETYERLEADKKKQVHKKRKCPGPIITYHSVTVPLVGEPGPKEENVDVEGLDPTPTASALTPHAGTGPV
Retrocopy SLETYERLEADKKKQVHKKRKCPGPIITYHSVTVPLVGEPGPKEENVDVEGLDPTPTASALTPHAGTGPV

Parental  VPPPRCSRTFITFSDDATFEEW-FPQGRPPKVPVREVCPVTHRPALYRDPVTDIPYATARAFKIIREAY
          V.PPRC..TFI.FSDDATFEEW.FPQGRPPKVPVREVCPVTHRPALYRDPVTDIPY.TARAFKIIREAY
Retrocopy VSPPRCLHTFIIFSDDATFEEW>FPQGRPPKVPVREVCPVTHRPALYRDPVTDIPYTTARAFKIIREAY

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	54.39 RPM
SRP017611_brain	0.00 RPM	31.12 RPM
SRP017611_kidney	0.00 RPM	39.03 RPM
SRP017611_liver	0.00 RPM	9.14 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_807 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_807 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000824	1 retrocopy	retro_amel_1768,
Canis familiaris	ENSCAFG00000012540	1 retrocopy	retro_cfam_807 ,
Equus caballus	ENSECAG00000017754	1 retrocopy	retro_ecab_13,
Echinops telfairi	ENSETEG00000004257	1 retrocopy	retro_etel_101,
Mustela putorius furo	ENSMPUG00000004027	1 retrocopy	retro_mputfur_1542,
Mus musculus	ENSMUSG00000008958	1 retrocopy	retro_mmus_1570,