RetrogeneDB ID: retro_cfam_1168

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:34055720..34056066(+)
• Located in intron of: ENSCAFG00000009139

Retrocopy information

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

Parental gene information

• Parental gene symbol: MNF1
• Ensembl ID: ENSCAFG00000031270
• Aliases: MNF1, C12H6orf125
• Description: mitochondrial nucleoid factor 1 [Source:HGNC Symbol;Acc:21237]

Sequence

>retro_cfam_1168
GAACAGGGCCGAGACTTTTGTGCTTACCTGCAGCACCAGGTAGCACAGGCCTTTCAGGAGGGAGAGAACACCCAGATTGC
AGAGCATGAGGCCTGTGGTCAGGTGTATGAGAGCTTAGCCACGACTCCATTCAAACTATTACAAACACCAATATTCTTGC
CCCAGAGACATGAGTTTCATCAGCCTGTCCATGGAAGAGTATAAGCTGATCCTGTGCACAGGCACCCTGAAAGAGTTTAA
GGAAACAAATAAAGATATATGGAAGACAGTGCAGGAGAAGTTTGCCCCCAGGAATCCCAAGGAGAAGCAGAGGGCCCAGG
CTCAGTCTTTATCTCACCCATGCACC

Alignment

ORF - retro_cfam_1168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRGRDLGTYLRQRVAQAFREGENTQIAEPEACDQMYESLA-RLHSNYYKHKYPRPRDTSFSGLSVEEYKL
          ..GRD...YL...VAQAF.EGENTQIAE.EAC.Q.YESLA.RLHSNYYKH.Y..PRD.SF..LS.EEYKL
Retrocopy EQGRDFCAYLQHQVAQAFQEGENTQIAEHEACGQVYESLA>RLHSNYYKHQYSCPRDMSFISLSMEEYKL

Parental  ILSTDTLEEFKEMNKGMWKKLQEKFAPRNTEEKQKAWARSLSRPHT
          IL.T.TL.EFKE.NK..WK..QEKFAPRN..EKQ.A.A.SLS.P.T
Retrocopy ILCTGTLKEFKETNKDIWKTVQEKFAPRNPKEKQRAQAQSLSHPCT

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	31.12 RPM
SRP017611_brain	0.00 RPM	14.45 RPM
SRP017611_kidney	0.00 RPM	57.45 RPM
SRP017611_liver	0.00 RPM	21.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1168 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1168 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031270	1 retrocopy	retro_cfam_1168 ,
Dasypus novemcinctus	ENSDNOG00000002019	1 retrocopy	retro_dnov_674,
Echinops telfairi	ENSETEG00000006979	2 retrocopies	retro_etel_1912, retro_etel_2009,
Macropus eugenii	ENSMEUG00000005278	3 retrocopies	retro_meug_1335, retro_meug_2027, retro_meug_337,
Monodelphis domestica	ENSMODG00000013996	1 retrocopy	retro_mdom_515,
Mustela putorius furo	ENSMPUG00000003032	1 retrocopy	retro_mputfur_511,
Mus musculus	ENSMUSG00000024208	2 retrocopies	retro_mmus_2543, retro_mmus_3376,
Otolemur garnettii	ENSOGAG00000015604	2 retrocopies	retro_ogar_2127, retro_ogar_2204,
Tupaia belangeri	ENSTBEG00000001380	6 retrocopies	retro_tbel_1486, retro_tbel_1573, retro_tbel_1754, retro_tbel_3269, retro_tbel_361, retro_tbel_994,