RetrogeneDB ID: retro_cfam_815

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:9542715..9543296(-)
• Located in intron of: ENSCAFG00000003556

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF13
• Ensembl ID: ENSCAFG00000008370
• Aliases: None
• Description: ring finger protein 13 [Source:HGNC Symbol;Acc:10057]

Sequence

>retro_cfam_815
ATGCTCATGCTGTTGGCCACACAAATATGTGGCATATTGACTGTCCAGCTCTTCGTATTCTTAAACCTACTACCTGTAGA
ATCAGGCATTTTAGCATGTAATTTTGAAAGTGCATCTCAGACATTTGATGACCTTCCAGTAAGATTTGGTTATAGACTTC
CAGCTGAAAGTTTAAGGGGTTCTTTGATTAACTCAAAACCAGAGAATGCCTATGAACCCACAGGGCCTCCACCACTGAAG
ACGATTCATCTGGCACTTTCATTGTGTTAGTTAGAAGACTTTGTGTAATTTTGATGTAGAGGTTTTAAAAGCACCAAGAG
CAGGATACAAAGCCGCCATAGTTCACAATTCTGATGACCTCAATAGCGTGGCACCCGGCGACTTTAATGTGCTAAATAAA
GTGGACATTCCATGTGTTTTATGGGGGAGTTATCAGCTAATGCCCTGAAAGATGAATTCACATTGAAAAAAGGGGCCACA
TCATCTTAGTTCTAGAATTCAGTGTGTCTCTGGACATTTACTACCTAAATCCCCTTTTTATTGCAATGTGTATCTGCCTT
GTCTTGATTGTCCTTTTCATA

Alignment

ORF - retro_cfam_815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.14 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLMLSATQVYTILTVQLFAFLNLLPVEADILAYNFENASQTFDDLPARFGYRLPAEGLKGFLINSKPENA
          MLML.ATQ...ILTVQLF.FLNLLPVE..ILA.NFE.ASQTFDDLP.RFGYRLPAE.L.G.LINSKPENA
Retrocopy MLMLLATQICGILTVQLFVFLNLLPVESGILACNFESASQTFDDLPVRFGYRLPAESLRGSLINSKPENA

Parental  CEPIVPPPLK-DNSSGTFIVLIRRLD-CNFDIKVLNAQRAGYKAAIVHNVDSDDLISMGSNDIDVLKKID
          .EP..PPPLK.D.SSGTFIVL.RRL..CNFD..VL.A.RAGYKAAIVHN..SDDL.S....D..VL.K.D
Retrocopy YEPTGPPPLK<DDSSGTFIVLVRRLC<CNFDVEVLKAPRAGYKAAIVHN--SDDLNSVAPGDFNVLNKVD

Parental  IPSV-FIGESSANSLKDEFTYEKG-GHIILVPEFSLPLE-YYLIPFLIIVGICLILIVIFM
          IP.V.F.GE.SAN.LKDEFT..KG.GHIILV.EFS..L..YYL.P..I...ICL.LIV.F.
Retrocopy IPCV<FMGELSANALKDEFTLKKG<GHIILVLEFSVSLDIYYLNPLFIAMCICLVLIVLFI

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	60.65 RPM
SRP017611_brain	0.00 RPM	98.21 RPM
SRP017611_kidney	0.00 RPM	180.48 RPM
SRP017611_liver	0.00 RPM	41.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_815 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_815 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_815 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010433	1 retrocopy	retro_amel_311,
Canis familiaris	ENSCAFG00000008370	1 retrocopy	retro_cfam_815 ,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dasypus novemcinctus	ENSDNOG00000014687	1 retrocopy	retro_dnov_139,
Microcebus murinus	ENSMICG00000001221	1 retrocopy	retro_mmur_323,
Nomascus leucogenys	ENSNLEG00000003149	1 retrocopy	retro_nleu_627,
Pongo abelii	ENSPPYG00000014202	1 retrocopy	retro_pabe_2392,