RetrogeneDB ID: retro_cfam_2117

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:98866874..98867291(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC8
• Ensembl ID: ENSCAFG00000019922
• Aliases: None
• Description: ER membrane protein complex subunit 8 [Source:HGNC Symbol;Acc:7864]

Sequence

>retro_cfam_2117
GAGGTGGCCCTCACGCTGATTGATTCATGGTGCAAAGATAATAGCTATGTGATTGCTGGTTATTATCAAGCTAATGAACG
AGTCAAGGATGCCAGTCTGAACCGGGTCGCAGAAAAGGTGGCCTCCAGAATCACCGAGGGCTTCAGCGATACTGCTCTCA
TCATGGTAGACAACACTAAGTTTACGATGGACTGCGTGGTGCCTACAATCCATGTGTACGAACCCCATGAAAACAGATGG
CGGTGCAGGGACCCACACTATAATTACTGTGAAGACTGGCCAGAGGCCCAGAGGATCTCAGCGTCACTCTTGGACAGCCG
GTCCTACGAAACACTTGTGGATTTCGACAACCACCTGGATGACATTCGGAATGACTGGACAAACCCAGAGATCAATAAAG
CCGTTCTACACCTGTGC

Alignment

ORF - retro_cfam_2117 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.4 %
• Parental protein coverage: 66.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVALTLIDSWCKDNSYVIAGYYQANERVKDASPNQVAEKVASRIAEGFSDTALIMVDNTKFTMDCVVPTI
          EVALTLIDSWCKDNSYVIAGYYQANERVKDAS.N.VAEKVASRI.EGFSDTALIMVDNTKFTMDCVVPTI
Retrocopy EVALTLIDSWCKDNSYVIAGYYQANERVKDASLNRVAEKVASRITEGFSDTALIMVDNTKFTMDCVVPTI

Parental  HVYEHHENRWRCRDPHYDYCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHLC
          HVYE.HENRWRCRDPHY.YCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHLC
Retrocopy HVYEPHENRWRCRDPHYNYCEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHLC

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	11.93 RPM
SRP017611_brain	0.00 RPM	10.88 RPM
SRP017611_kidney	0.00 RPM	29.25 RPM
SRP017611_liver	0.00 RPM	6.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2117 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2117 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019922	1 retrocopy	retro_cfam_2117 ,
Callithrix jacchus	ENSCJAG00000017312	1 retrocopy	retro_cjac_675,
Erinaceus europaeus	ENSEEUG00000011856	1 retrocopy	retro_eeur_44,
Macropus eugenii	ENSMEUG00000009360	5 retrocopies	retro_meug_1050, retro_meug_1386, retro_meug_636, retro_meug_709, retro_meug_97,
Monodelphis domestica	ENSMODG00000004596	1 retrocopy	retro_mdom_163,
Otolemur garnettii	ENSOGAG00000010372	1 retrocopy	retro_ogar_2503,