RetrogeneDB ID: retro_cfam_665

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:48056750..48057602(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000007865
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSCAFG00000005502
• Aliases: None
• Description: Canis lupus familiaris voltage-dependent anion channel 3 (VDAC3), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001251965]

Sequence

>retro_cfam_665
GAGATGTGTAACACACCGACTTACTGTGACCTAGGAAAGGCTGCCAAGGATGTCTTCAATAAAGGATATGGATTCGGCAT
GGTCAAAATAGACCTGAGAACCAAGTCTTGTAGTGGAGTGGAATTTTCTACTTCTGGTCATGCTTACACTGATACAGGGA
AAGCGTCAGGCAACCTAGAGACCAAATATAAGGTCTGTAACTATGGACTTACTTTCACCCAGAAATGGAACACAGACAAT
ACTCTTGGAACAGAAATCTCTTTGGAGAATAAGTTGGCTGAAGGGTTGAAACTGACTCTTGATACCATATTTGTACCGAA
CACAGGAAAGAAGAGTGGAAAATTGAAGGCTTCCTATAAACGAGATTGTTTCAGTGTTGGCAGTAATGTTGATATAGATT
TTTCTGGACCAACCATCTATGGCTGGGCTGTGTTAGCCTTTGAAGGTTGGCTTGCTGGCTATCAGATGAGTTTTGACACA
GCCAAATTCAAACTGTCACAGAATAATTTTGCCCTGGGTTACAAGGCTGCAGACTTCCAGCTGCACACTCATGTGAATGA
TGGCACTGAATTTGGAGGGTCTATCTACCAGAAGGTTAATGAGAAGATTGAAACATCAATAAACCTTGCTTGGACAGCCG
GCAGTAACAATACCCATTTTGGCATCGCTGCTAAATACAAGCTGGATTGTAGAACTTCTCTATCTGCTAAAGTAAACAAT
GCCAGCCTGATTGGACTGGGTTATACTCAGACTCTTCGACCAGGAGTCAAACTGACCCTATCAGCTTTAATCGACGGAAA
GAACTTCAATGCAGGAGGTCACAAGGTTGGGTTGGGATTTGAACTAGAAGCT

Alignment

ORF - retro_cfam_665 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.3 %
• Parental protein coverage: 97.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGL
          EMCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGL
Retrocopy EMCNTPTYCDLGKAAKDVFNKGYGFGMVKIDLRTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCNYGL

Parental  TFTQKWNTDNTLGTEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSVGSNVDIDFSGPTIY
          TFTQKWNTDNTLGTEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSVGSNVDIDFSGPTIY
Retrocopy TFTQKWNTDNTLGTEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSVGSNVDIDFSGPTIY

Parental  GWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLA
          GWAVLAFEGWLAGYQMSFDTAK.KLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLA
Retrocopy GWAVLAFEGWLAGYQMSFDTAKFKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLA

Parental  WTAGSNNTRFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGF
          WTAGSNNT.FGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGF
Retrocopy WTAGSNNTHFGIAAKYKLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLSALIDGKNFNAGGHKVGLGF

Parental  ELEA
          ELEA
Retrocopy ELEA

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	1.93 RPM	70.43 RPM
SRP017611_brain	11.27 RPM	47.32 RPM
SRP017611_kidney	18.49 RPM	69.80 RPM
SRP017611_liver	0.51 RPM	20.01 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_665 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM540362	48056810	48057210	99.5	398	2	396

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000000985	1 retrocopy	retro_cfam_1728,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665 , retro_cfam_713,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,