RetrogeneDB ID: retro_cfam_1861

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:69705026..69705548(+)
• Located in intron of: ENSCAFG00000018478

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB10
• Ensembl ID: ENSCAFG00000019476
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa [Source:HGNC Symbol;Acc:7696]

Sequence

>retro_cfam_1861
ATGCCGGACAGCTGGGACAAGGACATGTACCCCAGGTTCCCGCGCCGCACGCCGGCGCCCTCGCCGCAGACCTCGGTGCC
CAACCCCATAACCTATTTGACGAAGGCCTTCAACCTCCTCGTGGACCGGCCGGTGACCCTAGTGAGAGAGTTTATAGATC
GGCAGCATGCAAAGAACAGGTATTACTACTACCACCGGGAGTTCTGCCATGTGCCAGACATCACGGGGTGCCAGGAAAAG
GATGTCTTGTGCATGTTTGAAGCAGAAATGCAATAGAGAAGAGACTATAAAGTGGATCAAGAAATCATCAACATTATCTA
GGAGAGGCTGAAGGCCTGTCAGCAGCGGGAAGGTGAGAGCTACAGGCAGAACTGTGCCAAGGAGCTGGAGCAGTTCACCC
AGGGGGCCAAGGCCTGCCGGGACCACTATCACGACCTGGGAGCCCATTATTCTGCCAGGAAGTGCCTGGCTAAACAGAAG
CAGTGGATGCTGGCAGAGAGAAAAGCTGCTAAAGAGGCCGCC

Alignment

ORF - retro_cfam_1861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPDSWDKDVYPEPPRRTPAPSPQTSVPNPVTYLTKAFDVLVDRPVTLVREFIDRQHAKNRYYYYHREFRR
          MPDSWDKD.YP..PRRTPAPSPQTSVPNP.TYLTKAF..LVDRPVTLVREFIDRQHAKNRYYYYHREF..
Retrocopy MPDSWDKDMYPRFPRRTPAPSPQTSVPNPITYLTKAFNLLVDRPVTLVREFIDRQHAKNRYYYYHREFCH

Parental  VPDITECQEKDVLCMFEAEMQWRRDYKVDQEIVNIIQERLKACQQREGESYRQNCAKELEQFTQVAKAYQ
          VPDIT.CQEKDVLCMFEAEMQ.RRDYKVDQEI.NII.ERLKACQQREGESYRQNCAKELEQFTQ.AKA..
Retrocopy VPDITGCQEKDVLCMFEAEMQ*RRDYKVDQEIINII*ERLKACQQREGESYRQNCAKELEQFTQGAKACR

Parental  DRYHDLGAHYSARKCLAKQKQRMLAERKAAKEAA
          D.YHDLGAHYSARKCLAKQKQ.MLAERKAAKEAA
Retrocopy DHYHDLGAHYSARKCLAKQKQWMLAERKAAKEAA

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	84.42 RPM
SRP017611_brain	0.48 RPM	41.60 RPM
SRP017611_kidney	1.06 RPM	93.64 RPM
SRP017611_liver	0.36 RPM	30.82 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1861 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1861 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019476	1 retrocopy	retro_cfam_1861 ,
Echinops telfairi	ENSETEG00000017154	1 retrocopy	retro_etel_1955,
Felis catus	ENSFCAG00000011738	1 retrocopy	retro_fcat_307,
Homo sapiens	ENSG00000140990	2 retrocopies	retro_hsap_1573, retro_hsap_3801,
Gorilla gorilla	ENSGGOG00000009367	2 retrocopies	retro_ggor_1198, retro_ggor_2555,
Latimeria chalumnae	ENSLACG00000013152	1 retrocopy	retro_lcha_100,
Macaca mulatta	ENSMMUG00000029268	1 retrocopy	retro_mmul_2218,
Mus musculus	ENSMUSG00000040048	1 retrocopy	retro_mmus_2566,
Nomascus leucogenys	ENSNLEG00000008867	1 retrocopy	retro_nleu_1740,
Pongo abelii	ENSPPYG00000006974	2 retrocopies	retro_pabe_1297, retro_pabe_3106,
Pan troglodytes	ENSPTRG00000007618	2 retrocopies	retro_ptro_1060, retro_ptro_2578,
Rattus norvegicus	ENSRNOG00000014568	1 retrocopy	retro_rnor_1056,
Sus scrofa	ENSSSCG00000030328	1 retrocopy	retro_sscr_689,