RetrogeneDB ID: retro_cfam_1967

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:62425722..62425965(-)
• Located in intron of: ENSCAFG00000017591

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAM16
• Ensembl ID: ENSCAFG00000019226
• Aliases: PAM16, MAGMAS, TIMM16
• Description: Canis lupus familiaris presequence translocase-associated motor 16 homolog (S. cerevisiae) (PAM16), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001003391]

Sequence

>retro_cfam_1967
GGATGGGCTTGACACCAATCTGTGGCTACCTCCAACCTGTCCAGCCTCAGCCTCCAGGAGGCCCAGCAGAGTCCCCAAGT
CTCCAAGCTGAGCCCCAAGGAGATCCAGAAGAACTATGAACACCTATTCAAAGCGAATGATGTATCTGTGGGTGGCTCCT
ACCTGTGGTCCAAGGTGGCCTGAGCTGAGGAGCTCAGGATCCAGGCCCAGGAGGACAGAGAGAAGGAACAGATGCCTAAC
ACG

Alignment

ORF - retro_cfam_1967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.22 %
• Parental protein coverage: 69.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRAGHQSAAASNLSGLSLQEAQQILNVSKLSPEEIQKNYEHLFKVNDKSVGGSFYLQSKVVRAWERLQEE
          G.A.HQS.A.SNLS.LSLQEAQQ...VSKLSP.EIQKNYEHLFK.ND.SVGGS.YL.SKV..A.E.....
Retrocopy GWA*HQSVATSNLSSLSLQEAQQSPQVSKLSPKEIQKNYEHLFKANDVSVGGS-YLWSKVA*AEEL---R

Parental  LRIQAQEDREKEQMPKT
          ...Q.....E..QMP.T
Retrocopy IQAQEDREKE--QMPNT

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	0.13 RPM	27.72 RPM
SRP017611_brain	0.16 RPM	10.32 RPM
SRP017611_kidney	0.07 RPM	32.56 RPM
SRP017611_liver	0.07 RPM	9.43 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1967 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1967 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1967 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009200	1 retrocopy	retro_btau_1664,
Canis familiaris	ENSCAFG00000019226	1 retrocopy	retro_cfam_1967 ,
Callithrix jacchus	ENSCJAG00000019772	1 retrocopy	retro_cjac_1148,
Dasypus novemcinctus	ENSDNOG00000010921	2 retrocopies	retro_dnov_1361, retro_dnov_8,
Dipodomys ordii	ENSDORG00000014888	1 retrocopy	retro_dord_81,
Equus caballus	ENSECAG00000019387	1 retrocopy	retro_ecab_302,
Erinaceus europaeus	ENSEEUG00000007432	7 retrocopies	retro_eeur_138, retro_eeur_171, retro_eeur_213, retro_eeur_234, retro_eeur_273, retro_eeur_440, retro_eeur_673,
Echinops telfairi	ENSETEG00000006416	1 retrocopy	retro_etel_2070,
Felis catus	ENSFCAG00000027971	1 retrocopy	retro_fcat_520,
Myotis lucifugus	ENSMLUG00000008921	6 retrocopies	retro_mluc_2446, retro_mluc_2447, retro_mluc_2448, retro_mluc_2516, retro_mluc_2517, retro_mluc_429,
Mus musculus	ENSMUSG00000014301	1 retrocopy	retro_mmus_73,
Rattus norvegicus	ENSRNOG00000004608	1 retrocopy	retro_rnor_713,
Sus scrofa	ENSSSCG00000007947	2 retrocopies	retro_sscr_1090, retro_sscr_468,
Ictidomys tridecemlineatus	ENSSTOG00000003461	1 retrocopy	retro_itri_1732,
Tupaia belangeri	ENSTBEG00000001347	1 retrocopy	retro_tbel_3190,
Tarsius syrichta	ENSTSYG00000009306	1 retrocopy	retro_tsyr_282,