RetrogeneDB ID: retro_cfam_514

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:26294125..26294823(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000002473
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TDRKH
• Ensembl ID: ENSCAFG00000012856
• Aliases: None
• Description: tudor and KH domain containing [Source:HGNC Symbol;Acc:11713]

Sequence

>retro_cfam_514
GGGCTCCGGCCCGGCCCAGAGCGCGACCTCAGCCTCTCTCACAGCCGGGGCGCGGTCGTCGTGGAGCGCCGGTGGCAGGT
GCCGCTGGCCGGAGAGGGCGGGAAGCCGCGCCTGCCCCGCGACACCGGGTCTACAGGCTGGTAGAAGACACGAAGCACGG
GCCCAGGGGCAGCCTGGAGCTCATCCTCACGCGGTCGGTGGAAGGACTGGGAGTCCGGGGTGACCTGGGCTCAGTGAAGA
AATCTTTGGGCCGGAATCGACTGCCACCTCCAGGTCTGGCTGTATATGCATCCCCTGAAAACAAGAAACTGTTTGAGGAG
GAGAAATTGCTAAGACAAGAAGGAAAATTAGAGAAAGTACAGACCAGGACAGGTGAGATGACAGTGAAATTTCTGAGACG
CTGTCACCTGGAGGTGGGGATGAAGAACAACGTCAAATGGGAACTAAATCCCGAAATAGTTGCCCGCCATTTCTTCAAAA
ATCTTGGTGTTGTGGTCGCCCCACAGGCATTAAAGTTACCAGAAGAGCCCATCACACGGTGGGGCGAGTCCAGGTGTGAG
GGGACGGTAAATGGACTTGACGCTGTGAGAGTACCCATGTCTGTGGTGAACTTTGAGAGGCCCAAGACCAAAAGATACAA
GTGCTGGTTAGCCCAGCAAGCTGCCAAGGGAATGGCCCCCACCAACTCCCAGACGATC

Alignment

ORF - retro_cfam_514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPPPGPERDFSLSHSRGTVIVERWWQVPLAGEGRKPRLHR-RHRVYRLVEDTKHGPRGGLELILTRSVEG
          G..PGPERD.SLSHSRG.V.VER.WQVPLAGEG.KPRL.R.RHRVYRLVEDTKHGPRG.LELILTRSVEG
Retrocopy GLRPGPERDLSLSHSRGAVVVERRWQVPLAGEGGKPRLPR<RHRVYRLVEDTKHGPRGSLELILTRSVEG

Parental  LGVRGDLVSVKKSLGRNRLLPQGLAVYASPENKKLFEEEKLLRQEGKLEKIQTRTGEMTVKFLRSCHLEV
          LGVRGDL.SVKKSLGRNRL.P.GLAVYASPENKKLFEEEKLLRQEGKLEK.QTRTGEMTVKFLR.CHLEV
Retrocopy LGVRGDLGSVKKSLGRNRLPPPGLAVYASPENKKLFEEEKLLRQEGKLEKVQTRTGEMTVKFLRRCHLEV

Parental  GMKNNIKWELNPEIVARHFFKNLGVVVAPHALKLPEEPITRWGEYWCEVTVNGLDTVRVPMSVVKFERPK
          GMKNN.KWELNPEIVARHFFKNLGVVVAP.ALKLPEEPITRWGE..CE.TVNGLD.VRVPMSVV.FERPK
Retrocopy GMKNNVKWELNPEIVARHFFKNLGVVVAPQALKLPEEPITRWGESRCEGTVNGLDAVRVPMSVVNFERPK

Parental  TKRYKYWLAQQAAKGMAPTNSQTI
          TKRYK.WLAQQAAKGMAPTNSQTI
Retrocopy TKRYKCWLAQQAAKGMAPTNSQTI

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	47.46 RPM
SRP017611_brain	0.00 RPM	34.85 RPM
SRP017611_kidney	0.07 RPM	46.23 RPM
SRP017611_liver	0.07 RPM	29.59 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_514 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_514 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012856	1 retrocopy	retro_cfam_514 ,
Oryctolagus cuniculus	ENSOCUG00000001387	1 retrocopy	retro_ocun_1361,
Otolemur garnettii	ENSOGAG00000001839	1 retrocopy	retro_ogar_1568,