RetrogeneDB ID: retro_cfam_1034

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:26884426..26884659(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP9
• Ensembl ID: ENSCAFG00000016162
• Aliases: None
• Description: signal recognition particle 9kDa [Source:HGNC Symbol;Acc:11304]

Sequence

>retro_cfam_1034
ATGCCGCAGTACCAGACCTGGGAGGAGTTCAGCTGCTCGGCCAAGAACTTCTACCTTCCCGATCCTATGAAGGCACGTGT
GGTTCTCAAATATAGGCCTTCTGAATGGAAGTTTCTGTATTAAAGTAACAGATGATTTAGTTTGTTTTGGTGTATAGAAC
AGACCAAGCCCAAGATGTAAAGAAGATTGAGAAATTCCACAGTCAACTAATGCGACGCGTGGTAGCCAAGGAA

Alignment

ORF - retro_cfam_1034 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.54 %
• Parental protein coverage: 89.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSD-GSLCIKVTDDLVC-LVYRTDQAQDVKKIEKFHSQ
          MPQYQTWEEFS..A...YL.DPMKARVVLKYR.S..GS.CIKVTDDLVC.LVYRTDQAQDVKKIEKFHSQ
Retrocopy MPQYQTWEEFSCSAKNFYLPDPMKARVVLKYRPSE>GSFCIKVTDDLVC>LVYRTDQAQDVKKIEKFHSQ

Parental  LMRLMVAKE
          LMR..VAKE
Retrocopy LMRRVVAKE

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	23.48 RPM
SRP017611_brain	0.00 RPM	16.83 RPM
SRP017611_kidney	0.00 RPM	19.02 RPM
SRP017611_liver	0.00 RPM	3.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1034 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1034 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016162	2 retrocopies	retro_cfam_1034 , retro_cfam_1527,
Dasypus novemcinctus	ENSDNOG00000013412	3 retrocopies	retro_dnov_1947, retro_dnov_2181, retro_dnov_742,
Echinops telfairi	ENSETEG00000012291	1 retrocopy	retro_etel_272,
Loxodonta africana	ENSLAFG00000004081	3 retrocopies	retro_lafr_1184, retro_lafr_377, retro_lafr_648,
Otolemur garnettii	ENSOGAG00000001752	1 retrocopy	retro_ogar_230,