RetrogeneDB ID: retro_cfam_1343

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:48891078..48891375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA2
• Ensembl ID: ENSCAFG00000005861
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7685]

Sequence

>retro_cfam_1343
ATGGCAGCTGCCACAGCGAGTCTGAGAATTGGGGCCAAAGTTGCCCCGCGTGAGATTCGTGTCCACTTGTGCCAGTGCTC
GCCCGGCAGTCAGGGCGTCAGGGAATTCATCGAGAAACACTATGTAGAGCTGAAGAAGGCGACTCCTGACCTGCCAATCC
TAACCAGCGAGTGTTCTGATGTGCAGCACAAACTCTGGACCCGCTACGCATTTGCCCGAGAGAAGAATGTCTCTTTGAAC
AGCCTGAGTGCTGATCAGGTAACCAGAGCCGTGGACAATGTGCTAAGTGGCAAAGCC

Alignment

ORF - retro_cfam_1343 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGAAASLRIGAKVGLREIRVHLCQRSSGSQGVREFIEKHYVELKKANPDLPILIRECSDVQPKLWARYA
          MA.A.ASLRIGAKV..REIRVHLCQ.S.GSQGVREFIEKHYVELKKA.PDLPIL..ECSDVQ.KLW.RYA
Retrocopy MAAATASLRIGAKVAPREIRVHLCQCSPGSQGVREFIEKHYVELKKATPDLPILTSECSDVQHKLWTRYA

Parental  FGQEKNVSLNNLSADQVTKAVENVLSGKA
          F..EKNVSLN.LSADQVT.AV.NVLSGKA
Retrocopy FAREKNVSLNSLSADQVTRAVDNVLSGKA

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	28.39 RPM
SRP017611_brain	0.00 RPM	24.93 RPM
SRP017611_kidney	0.00 RPM	68.81 RPM
SRP017611_liver	0.00 RPM	16.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1343 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1343 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015041	2 retrocopies	retro_btau_124, retro_btau_151,
Canis familiaris	ENSCAFG00000005861	1 retrocopy	retro_cfam_1343 ,
Cavia porcellus	ENSCPOG00000009178	2 retrocopies	retro_cpor_1045, retro_cpor_1290,
Latimeria chalumnae	ENSLACG00000005796	1 retrocopy	retro_lcha_48,
Mus musculus	ENSMUSG00000014294	1 retrocopy	retro_mmus_2579,
Nomascus leucogenys	ENSNLEG00000009325	1 retrocopy	retro_nleu_67,
Otolemur garnettii	ENSOGAG00000027727	1 retrocopy	retro_ogar_1633,
Pongo abelii	ENSPPYG00000015860	1 retrocopy	retro_pabe_938,
Rattus norvegicus	ENSRNOG00000017571	1 retrocopy	retro_rnor_262,
Sus scrofa	ENSSSCG00000014371	1 retrocopy	retro_sscr_48,
Tupaia belangeri	ENSTBEG00000005978	1 retrocopy	retro_tbel_2688,