RetrogeneDB ID: retro_cfam_1454

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 31:27227888..27228286(-)
• Located in intron of: ENSCAFG00000008978

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL27
• Ensembl ID: ENSCAFG00000017031
• Aliases: None
• Description: mitochondrial ribosomal protein L27 [Source:HGNC Symbol;Acc:14483]

Sequence

>retro_cfam_1454
GCCCTGCTGAGCCCCCCTTAGGCTGCGTCTCTTGCCGTCAGGTATGCATCCAAAAAGACAGGTGGCAGCTCCAAAAACCT
GGGAGGAAAGTCACCAGGCAAATGCTTTGGCCTCAGGAAAATGGAGGGTCACTACGTTGATGCTGGCAGCATCCTTGCAA
CTCAATGCCACTTCCGTTGGCACCCAGGAGCCCATGTGGGCCTTGGGAAGAAGAAGCACCTGTATGCCCTGGAGGAGGGA
GTGGTCGCCACACTAAGGAGGTCTATGTGCCCAGTCCCAGCAACACAGAGGCTGTGGAGCTGGTTACCAGGCTGCCCAAG
GGTGCTGTGCTCTATAAGACTTTTGTCCACGTGGTTCCTGTGAAGCCTGAGGGCACCTTCAAACTGGTAGCTATGCTT

Alignment

ORF - retro_cfam_1454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.03 %
• Parental protein coverage: 89.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALLSPPQAASLAVRYASKKTGGSSKNLGGKSPGKRFGLRKMEGHYVHAGNILATQRHFRWHPGAHVGLGK
          ALLSPP.AASLAVRYASKKTGGSSKNLGGKSPGK.FGLRKMEGHYV.AG.ILATQ.HFRWHPGAHVGLGK
Retrocopy ALLSPP*AASLAVRYASKKTGGSSKNLGGKSPGKCFGLRKMEGHYVDAGSILATQCHFRWHPGAHVGLGK

Parental  KKHLYALEEGVV-HYTKEVYVPSPSNTEAVELVTRLPKGAVLYKTFVHVVPVKPEGTFKLVAML
          KKHLYALEEGVV...TKEVYVPSPSNTEAVELVTRLPKGAVLYKTFVHVVPVKPEGTFKLVAML
Retrocopy KKHLYALEEGVV<RHTKEVYVPSPSNTEAVELVTRLPKGAVLYKTFVHVVPVKPEGTFKLVAML

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	25.79 RPM
SRP017611_brain	0.00 RPM	17.39 RPM
SRP017611_kidney	0.53 RPM	85.52 RPM
SRP017611_liver	0.58 RPM	17.77 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1454 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1454 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454 ,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233, retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696, retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,