RetrogeneDB ID: retro_cfam_1463

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:8222786..8224190(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000009155
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFKM
• Ensembl ID: ENSCAFG00000009035
• Aliases: PFKM, M-PFK
• Description: Canis lupus familiaris phosphofructokinase, muscle (PFKM), mRNA. [Source:RefSeq mRNA;Acc:NM_001003199]

Sequence

>retro_cfam_1463
AGGATGGGTGTGGAAGCAGTGATGGCACTCTTGGTGGGGACCCCGGACACCCCGGCCTGCTTGGTGAGCCTCTCTGGTAA
CCAGGCTGTGCACCTGCCCCTCATGGAGTGTGTGCAGGTGACCAAGGATGTGACCAAGGCCATGAACGCAGGAAATTCGA
TGAAGCCGTGAAGCTGAGAGGCCGGAGCTTCATGAACAACTGGGAGGTGTACAAGCTTCTGGCTCACATCAGACCTCCTG
TCTCGAAGACATTGGCTAGCATGCACATGGTGGCCGTGACGAACGTGGATGCCCCAGCCGCAGGCATGAATGCTGCCGTC
CACTCCACCATGAGAATTGGCCTCATCCAGGGCAACCGGGTGCTGGTTGTGCATGATGGCTTTGAGGGCCTAGCCAAGGG
TCAGATGGAGGAGGCTGGCTGGAGCTGTGTGGGGGGCTGGACTGGCCAAGGCGGTTCCAAACTTGGGACTAAGAGGACTC
TGCCCAAGAAGAGCTTTGAGCAGATCAGTGCCAACATCACTAAGTTTAACATTCAGGGCCTGATCATCATCGGGGGCTTT
GAGGCTTACACTGGGGGCCTGGAGCTGATGGAGGGGAAGGAAGCAGTTTGATGAGCTGTGCATCCCGTTAGTGCTCATCC
CTGCTATGGTGTCCAACAACGTCCCTGGCTCGGACTTCAGCGTGGGCACTGACACAGCCCTCTACACTATCTGCACGACC
TGTGACCGCATCAAGCAGTCAGCAGCAGGCACCAAGCGGCGGGTGTTCATCATTGAAACTATGGGTGGCTACTGCGGCTA
CCTGGCCACCATGGCAGGCCTGGCCACTGGGGCGGATGCTGCCTACATTTTTGAGGAGCCCTTCACCATTCGGGACCTGC
AGGCAAATGTTGAACATCTGGTGCAAAAGATGAAAACAACTGTGAAGAGGGGCCTGGTGTTAAGGAATGAGAAATGCAAT
GAGAACTATACCACAGACTTCATTTTCAACCTGTACTCTGAGGAGGGGAAGGGCATCTTCGACAGCAGGAAGAATGTGCT
CGGCCACATGCAGCAGGGTGGGAGCCCAACTCCGTTTGACAGGAATTTTGCCACTAAAATGGGCACCAAGGCTATGAACT
GGATGTCTGGGAAAATCAAAGAGAGTTACCGTGATGGGAGGATCTTTGCCAATACACCAGACTCGGGCTGTGTTCTGGGG
ATGCGTAAGAGGGCTCTGGTCTTTCAACCAGTGACTGAGCTGAAGGACCAGACAGATTTTGATCACCACATCCCCAAGGA
ACAGTGGCGGCTGAAGCTGAGGCCCATCCTCAAAATCCTAGCCAAGTACGAGATTGACTTGGACACCACAGAGCATGCCC
ACCTGGAGCACATCAGTCGGAAGCGATCTGGAGAAACTTCTATC

Alignment

ORF - retro_cfam_1463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.47 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RMGVEAVMALLEGTPDTPACVVSLSGNQAVRLPLMECVQVTKDVTKAMND-RKFDEAMKLRGRSFMNNWE
          RMGVEAVMALL.GTPDTPAC.VSLSGNQAV.LPLMECVQVTKDVTKAMN..RKFDEA.KLRGRSFMNNWE
Retrocopy RMGVEAVMALLVGTPDTPACLVSLSGNQAVHLPLMECVQVTKDVTKAMNA<RKFDEAVKLRGRSFMNNWE

Parental  VYKLLAHIRPPVSKTSATMHTVAVMNVGAPAAGMNAAVRSTVRIGLIQGNRVLVVHDGFEGLAKGQIEEA
          VYKLLAHIRPPVSKT.A.MH.VAV.NV.APAAGMNAAV.ST.RIGLIQGNRVLVVHDGFEGLAKGQ.EEA
Retrocopy VYKLLAHIRPPVSKTLASMHMVAVTNVDAPAAGMNAAVHSTMRIGLIQGNRVLVVHDGFEGLAKGQMEEA

Parental  GWSYVGGWTGQGGSKLGTKRTLPKKSFEQISANITKFNIQGLIIIGGFEAYTGGLELMEG-RKQFDELCI
          GWS.VGGWTGQGGSKLGTKRTLPKKSFEQISANITKFNIQGLIIIGGFEAYTGGLELMEG.RKQFDELCI
Retrocopy GWSCVGGWTGQGGSKLGTKRTLPKKSFEQISANITKFNIQGLIIIGGFEAYTGGLELMEG>RKQFDELCI

Parental  PFVVIPATVSNNVPGSDFSVGADTALNTICTTCDRIKQSAAGTKRRVFIIETMGGYCGYLATMAGLAAGA
          P.V.IPA.VSNNVPGSDFSVG.DTAL.TICTTCDRIKQSAAGTKRRVFIIETMGGYCGYLATMAGLA.GA
Retrocopy PLVLIPAMVSNNVPGSDFSVGTDTALYTICTTCDRIKQSAAGTKRRVFIIETMGGYCGYLATMAGLATGA

Parental  DAAYIFEEPFTIRDLQANVEHLVQKMKTTVKRGLVLRNEKCNENYTTDFIFNLYSEEGKGIFDSRKNVLG
          DAAYIFEEPFTIRDLQANVEHLVQKMKTTVKRGLVLRNEKCNENYTTDFIFNLYSEEGKGIFDSRKNVLG
Retrocopy DAAYIFEEPFTIRDLQANVEHLVQKMKTTVKRGLVLRNEKCNENYTTDFIFNLYSEEGKGIFDSRKNVLG

Parental  HMQQGGSPTPFDRNFATKMGAKAMNWMSGKIKESYRNGRIFANTPDSGCVLGMRKRALVFQPVTELKDQT
          HMQQGGSPTPFDRNFATKMG.KAMNWMSGKIKESYR.GRIFANTPDSGCVLGMRKRALVFQPVTELKDQT
Retrocopy HMQQGGSPTPFDRNFATKMGTKAMNWMSGKIKESYRDGRIFANTPDSGCVLGMRKRALVFQPVTELKDQT

Parental  DFDHRIPKEQWWLKLRPILKILAKYEIDLDTTEHAHLEHISRKRSGETSI
          DFDH.IPKEQW.LKLRPILKILAKYEIDLDTTEHAHLEHISRKRSGETSI
Retrocopy DFDHHIPKEQWRLKLRPILKILAKYEIDLDTTEHAHLEHISRKRSGETSI

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	272.45 RPM
SRP017611_brain	0.16 RPM	280.33 RPM
SRP017611_kidney	0.07 RPM	49.00 RPM
SRP017611_liver	0.00 RPM	2.25 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1463 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1463 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009035	1 retrocopy	retro_cfam_1463 ,
Microcebus murinus	ENSMICG00000009077	1 retrocopy	retro_mmur_970,
Otolemur garnettii	ENSOGAG00000005501	1 retrocopy	retro_ogar_1984,