RetrogeneDB ID: retro_cfam_887

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:15655862..15656122(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000016594
• Aliases: None
• Description: None

Sequence

>retro_cfam_887
ATATCTCAGGCAAATGGGGACACAGGGGTGGGGGTAGGGGCGCGAGAGGGCACTGCTGCTGTGGACCCCTTCGGCTTCAG
CCCAGAGCCCACACCTGAGGACATCTGCTGCCTTCATTCCGAGTTTGCTGCTGAACAGGACTGAGGCTAGTTCCACCAGA
CTCGGAGCCTCCTATCGGCCTTTGTGGGGGGTCTGGGGAGTTCATGGATCCCTTTCAGTAGAAGCCCGATAAGGAGACTG
GCCCCCAAGCCTGGTGCCCC

Alignment

ORF - retro_cfam_887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 50.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRANGDAR-GDTVGNGTAAASPFSFSPEPTLEDIRRLHAEFAAERDWGQFHQPRNLLLALVGEV-GELA
          .S.ANGD...G.....GTAA..PF.FSPEPT.EDI..LH.EFAAE.D.G.FHQ.R.LL.A.VG...GE..
Retrocopy ISQANGDTGVGVGAREGTAAVDPFGFSPEPTPEDICCLHSEFAAEQD*G*FHQTRSLLSAFVGGL<GEFM

Parental  ELFQWKPDEEPGPQAWSP
          ..FQ.KPD.E.GPQAW.P
Retrocopy DPFQ*KPDKETGPQAWCP

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	9.07 RPM
SRP017611_brain	0.00 RPM	3.81 RPM
SRP017611_kidney	0.00 RPM	2.97 RPM
SRP017611_liver	0.00 RPM	1.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_887 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_887 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016594	1 retrocopy	retro_cfam_887 ,
Callithrix jacchus	ENSCJAG00000002621	2 retrocopies	retro_cjac_43, retro_cjac_676,
Myotis lucifugus	ENSMLUG00000013774	1 retrocopy	retro_mluc_1052,
Otolemur garnettii	ENSOGAG00000011361	1 retrocopy	retro_ogar_874,
Rattus norvegicus	ENSRNOG00000017850	2 retrocopies	retro_rnor_1173, retro_rnor_2626,
Sus scrofa	ENSSSCG00000007796	1 retrocopy	retro_sscr_676,