RetrogeneDB ID: retro_cfam_2005

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:39687518..39687909(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP2
• Ensembl ID: ENSCAFG00000000456
• Aliases: None
• Description: THAP domain containing, apoptosis associated protein 2 [Source:HGNC Symbol;Acc:20854]

Sequence

>retro_cfam_2005
AATTGTGCAGCAGCAGGCTGTGCTACTACCCACAACACACATGTTAACATCAGCTTCCACAGGTTTCGTCTGGATCCTAA
AAGAAGAAAAGAATGGGCTTGCCAGCTTAGACACAACAATTTTGTGCCAAGAAAACACACTTTTCTTTGTTCAAAGCACT
TTGAAGCCTCCTGTTTTGACTCAACAGGACAAACTCGGTGACTTAAAATGGATGCAATTCCAACCATTTTTTATTTTTAT
ACCCATTGAAAGTCTATGAAACTCAAATCAAGGAATCTTTTGAAGAAAAACAACAGTTGTACTCCAACAGAACCATCTAC
TTTAAGATCAAACCTTAGTAGTTATCAAGTACTACTTGAACACAGTTACTGCTTTTAGGAATCCTATGGAG

Alignment

ORF - retro_cfam_2005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 60.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NCAAAGCATTYDKHINISFHRFPLDPKRRKEWIRLLRRKNFVPGKHTFLCSKHFEASCFDLTGQTRRLKM
          NCAAAGCATT...H.NISFHRF.LDPKRRKEW...LR..NFVP.KHTFLCSKHFEASCFD.TGQTR.LKM
Retrocopy NCAAAGCATTHNTHVNISFHRFRLDPKRRKEWACQLRHNNFVPRKHTFLCSKHFEASCFDSTGQTR*LKM

Parental  DAVPTIFDFCTHLKSMKLKSRNLLKKNNNCTPKGPSNLKPNISSQQVLLEHSY-AFRNPME
          DA.PTIF.F.TH.KSMKLKSRNLLKKNN.CTP..PS.L..N.SS.QVLLEHSY.AFRNPME
Retrocopy DAIPTIFYFYTH*KSMKLKSRNLLKKNNSCTPTEPSTLRSNLSSYQVLLEHSY>AFRNPME

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	6.13 RPM
SRP017611_brain	0.00 RPM	2.78 RPM
SRP017611_kidney	0.00 RPM	2.38 RPM
SRP017611_liver	0.00 RPM	0.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2005 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2005 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2005 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000456	1 retrocopy	retro_cfam_2005 ,
Canis familiaris	ENSCAFG00000003290	1 retrocopy	retro_cfam_1931,
Mustela putorius furo	ENSMPUG00000017487	2 retrocopies	retro_mputfur_167, retro_mputfur_509,