RetrogeneDB ID: retro_cfam_1761

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:41108727..41109189(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JAZF1
• Ensembl ID: ENSCAFG00000003001
• Aliases: None
• Description: JAZF zinc finger 1 [Source:HGNC Symbol;Acc:28917]

Sequence

>retro_cfam_1761
GATACAGATCCAAGCGTTTTAGAACAAGAATTATAGCAGCCAACCTATGTTGCCCTCAGTTACGTGAATAGATTCATGAC
GGTTGCCACTTGCTGAGAGCCAGTCCCTAAAGAAGATTCACCTGAAGCTCTTGATGAGCTTGTCCAGCTCAGGGTCCTGA
AGGAATGTGTCCACTCCACCATGCCACAGCAGGGGAAGCCTTACTCCCCCCATTACTCTGCCCAACATCTCGTCCTCTTC
ATTCTGCAGCAACACCCCAACAGGCAGTGAGTACCACTGGGAGGAGGTGGATTATGAGGAATGGGACAGCGATGAGCCTG
GACCACAGAGAGTGCCATCAGCTCAGAAGCTATCCTCAGCTCCATGCACAAAAACGGAGAGGAAGAGAAGCCTTTTGTCT
GCCCGGTTCCTGGATGTAAAAAGAGATACAAGGTGAATGGTATAAAGTACCATGCTAAGGAC

Alignment

ORF - retro_cfam_1761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.62 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NTDPRVLEKQELQQPTYVALSYINRFMTDAA-RREQESLKKKIQPKLSLTLSSSVSRGNVSTPPRHSSGS
          .TDP.VLE.QEL.QPTYVALSY.NRFMT.A.....Q...K.......SL...SS.S..NVSTPP.HS.GS
Retrocopy DTDPSVLE-QEL*QPTYVALSYVNRFMTVAT>AESQSLKKIHLKLLMSLS--SSGS*RNVSTPPCHSRGS

Parental  LTPPVTPPITPSSSFRSSTPTGSEYDEEEVDYEESDSDE-SWTTESAISSEAILSSMCMNGGEEKPFACP
          LTPP.T.P...SSSF.S.TPTGSEY..EEVDYEE.DSDE..WTTESAISSEAILSSM..NG.EEKPF.CP
Retrocopy LTPPITLPNISSSSFCSNTPTGSEYHWEEVDYEEWDSDE<AWTTESAISSEAILSSMHKNGEEEKPFVCP

Parental  VPGCKKRYKNVNGIKYHAKN
          VPGCKKRYK.VNGIKYHAK.
Retrocopy VPGCKKRYK-VNGIKYHAKD

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	15.79 RPM
SRP017611_brain	0.00 RPM	14.13 RPM
SRP017611_kidney	0.00 RPM	2.05 RPM
SRP017611_liver	0.00 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1761 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1761 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003001	1 retrocopy	retro_cfam_1761 ,
Felis catus	ENSFCAG00000023035	1 retrocopy	retro_fcat_1660,
Otolemur garnettii	ENSOGAG00000029759	1 retrocopy	retro_ogar_770,