RetrogeneDB ID: retro_cfam_610

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:51177177..51177875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAFAH1B3
• Ensembl ID: ENSCAFG00000004847
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa) [Source:HGNC Symbol;Acc:8576]

Sequence

>retro_cfam_610
GCCAAGAAAAGTGAAGAGGAGAATGCACTGACAAGTCCATGCTGGTATGGGATGTGCAAGGTGACAGAGGCTGAATATCC
CTGAACCATTGGTTCATATCTGACAGCAAAGATAAGGAACATGAGGTACTGTTCATTGGAGACTCCTGGGTTCAGCTAAT
GTACCAGTGCAAGATCTGGCAGGAGCTCTTTTCCCCTCTGCATGCACTTAACTTTGGCATTGGCAGTGATAACACATAGC
AAGTGCTTTGGCAAGTGGAGAATGGGGAGCTGGAACAAATCCAACCCAAGATTATAGGGGTCTGGGTGGGTACTAACCAC
CACAGGCACACAGTGGAGCAAGTGACTGGCGGCATCAAGACCATCGTGCAACTGGTGAAGCAACAGCAGCCGCAGGCCCG
AGTGTTTGGTGCTGGGCTTGTTTCCCAGGGCCAGTATCCTAACCCACTTCATGAGAAAAACTGATAGATGAATGAGCTGG
TCCAGGCAGCACTGGCTGGCCACCCACAGGCCCACTTCCTAGATGCCAACTCTGGCTTTGTGCACTTAGATGGTACCATA
AGTCACCATGGCATGTACGAATACCTGCATCTGAACCATCTGGGCTACACAGCTGTCCACTGGGACTGGCACTCCCTGCT
TCTGCATATGCTGGCCCAAGACTAGGGCCAGGGTATCCCCTTGCCAGAGGCTAACCCC

Alignment

ORF - retro_cfam_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.94 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKMSGEENPASKPT-PVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQCEIWRELFSPLHA
          AK.S.EEN....P...V.DVQGD....SL.H.F..DSKDKE.EV.FIGDS.VQLM.QC.IW.ELFSPLHA
Retrocopy AKKSEEENALTSPC<LVWDVQGDRG*ISLNHWFISDSKDKEHEVLFIGDSWVQLMYQCKIWQELFSPLHA

Parental  LNFGIGSDSTQHVLWRLENGELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNQRQPQARVVVLG
          LNFGIGSD.T..VLW..ENGELE.I.PKI..VWVGTN.H.HT.EQVTGGIK.IVQLV.Q.QPQARV...G
Retrocopy LNFGIGSDNT*QVLWQVENGELEQIQPKIIGVWVGTNHHRHTVEQVTGGIKTIVQLVKQQQPQARVFGAG

Parental  LLPRGQHPNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRA
          L...GQ.PNPL.EKN...NELV.AALAGHP.AHFLDA..GFVH.DGTISHH.MY.YLHL..LGYT.V...
Retrocopy LVSQGQYPNPLHEKN**MNELVQAALAGHPQAHFLDANSGFVHLDGTISHHGMYEYLHLNHLGYTAVHWD

Parental  LHSLLLRLLAQDQGQGIPLPEATP
          .HSLLL..LAQD.GQGIPLPEA.P
Retrocopy WHSLLLHMLAQD*GQGIPLPEANP

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	63.38 RPM
SRP017611_brain	0.00 RPM	10.48 RPM
SRP017611_kidney	0.00 RPM	6.87 RPM
SRP017611_liver	0.00 RPM	1.52 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_610 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_610 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019787	1 retrocopy	retro_btau_547,
Canis familiaris	ENSCAFG00000004847	1 retrocopy	retro_cfam_610 ,
Canis familiaris	ENSCAFG00000013226	1 retrocopy	retro_cfam_1335,
Dasypus novemcinctus	ENSDNOG00000002870	1 retrocopy	retro_dnov_1276,
Macaca mulatta	ENSMMUG00000012172	1 retrocopy	retro_mmul_18,
Mustela putorius furo	ENSMPUG00000007574	1 retrocopy	retro_mputfur_351,
Rattus norvegicus	ENSRNOG00000020481	1 retrocopy	retro_rnor_976,