RetrogeneDB ID: retro_cfam_1380

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:47349048..47349866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX10
• Ensembl ID: ENSCAFG00000017899
• Aliases: None
• Description: cytochrome c oxidase assembly homolog 10 (yeast) [Source:HGNC Symbol;Acc:2260]

Sequence

>retro_cfam_1380
TCACAGCTCTCTGCCGGATTTGCACAGGCTCCAGGACCTCCTGACTGGCCCTGTTTCCTACTCAGTTCTGTCAGAACAGG
CCTTGCATTCTGCACTACCAACCCCATCCATCAGTTTTTTTGAGGCACCATTGGATTCAAAAGTGAACACGAGAAAAACA
AGCCTCTGGTTCATGGACAGATTAGCCCATGGCTAGCTGTGTCCTTTGCCACCTGCTGTGCTGTTCCATGAGTTGCCCTA
CTAACCTAGGGGGTGAACCCACTCGCGGGAGCCCTGAGGATCATCCACATTGTCCTGTATACCTGTCGCTATAACCCATT
GAAGAGGATCAGCATCACCAACATGTGGGTCAGAGCCATTGTTGGGGTCATCCCACCTGTCATGGATGGGACAGCTGCTA
CTGGGAGCCTCAATGCTGGAACATTTCTTCCCAGAAGAATCTTCTGCTCTTGCCAGTTTCTTCCATTTCAACGCCCTGAG
CTGGGGACTCTACACAGACTACTCTTGAGGCTTCCATTTGATATCGGTCACCCACCCAGCTCTGTGCAGATGCATCACTC
TGTACCACTGCCCAGCATGGATTGGACTGTTCTCGGGGCCCCATCCTGGACGTCACCATATGGACCTTTCCTGTCATCTC
CCTCCCCAATAACCTGTATATTTCCTACGTCAACTTTCAGTTCTACAGGAATGTGGACCCGAAGAGCTCCTGGAAACTGT
TCTTCTGCAGCCTCTAGCACCTGCCCTTGCTCCTGCTGCTCCTGCTCACCTGCAGGCAACCCCGAGGTGGGAATGGAGCC
AGGGTAGAGCCTCAGAGT

Alignment

ORF - retro_cfam_1380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.38 %
• Parental protein coverage: 62.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  STTSAGFALAPGPFDWPCFLLTSLGTGLASCAANSINQFF-EVPFDSNMN-RTKNRPLVRGQISPLLAVS
          S..SAGFA.APGP.DWPCFLL.S..TGLA.C..N.I.QFF.E.P.DS..N...KN.PLV.GQISP.LAVS
Retrocopy SQLSAGFAQAPGPPDWPCFLLSSVRTGLAFCTTNPIHQFF>EAPLDSKVN<HEKNKPLVHGQISPWLAVS

Parental  FATCCAVPGVALLTWGVNPLTGALGVFNIFLYTCCYTPLKRISIANTWVGAVVGAVPPVMGWTAATGSLD
          FATCCAVP.VALLT.GVNPL.GAL....I.LYTC.Y.PLKRISI.N.WV.A.VG..PPVM..TAATGSL.
Retrocopy FATCCAVP*VALLT*GVNPLAGALRIIHIVLYTCRYNPLKRISITNMWVRAIVGVIPPVMDGTAATGSLN

Parental  AGAFLLGGILYSWQFP-HFNALSWGLREDYSRGGYCMMSVTHPALCRRVALRHCLALIGLST-AAP-VLD
          AG.FL...I..S.QF..HFNALSWGL..DYS..G....SVTHPALCR...L.HC.A.IGL....AP..LD
Retrocopy AGTFLPRRIFCSCQFL>HFNALSWGLYTDYS-*GFHLISVTHPALCRCITLYHCPAWIGLFS<GAP<ILD

Parental  VTTWTFPVISLPINLYITYLGFRFYTDADRKSSRKLFFCSLWHLPLLLLLMLTCKRPPGARGAGAEPQS
          VT.WTFPVISLP.NLYI.Y..F.FY...D.KSS.KLFFCSL.HLPLLLLL.LTC..P.G..GA..EPQS
Retrocopy VTIWTFPVISLPNNLYISYVNFQFYRNVDPKSSWKLFFCSL*HLPLLLLLLLTCRQPRGGNGARVEPQS

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	13.36 RPM
SRP017611_brain	0.00 RPM	16.75 RPM
SRP017611_kidney	0.00 RPM	19.02 RPM
SRP017611_liver	0.00 RPM	13.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1380 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015294	1 retrocopy	retro_btau_1425,
Canis familiaris	ENSCAFG00000017899	1 retrocopy	retro_cfam_1380 ,
Callithrix jacchus	ENSCJAG00000004522	1 retrocopy	retro_cjac_3938,
Felis catus	ENSFCAG00000010334	1 retrocopy	retro_fcat_814,
Otolemur garnettii	ENSOGAG00000007457	1 retrocopy	retro_ogar_606,