RetrogeneDB ID: retro_rnor_262

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:184568697..184568997(-)
• Located in intron of: ENSRNOG00000015488

Retrocopy information

• Ensembl ID: ENSRNOG00000043512
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ndufa2
• Ensembl ID: ENSRNOG00000017571
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001099623]

Sequence

>retro_rnor_262
ATGGCGGCAGCTGCTGCAAGCCCAGTAGTCGGTGCAAAGCCAGCATTGCATGAGATTCACATTCACTTATGCCAGCGTTC
CCCAGGCAGCCAGGGTGGGAGGGATTTCATCCAGCAATGGTACGTGGAGCTGAAGAAGGTACACCCCGACCTGCCCATTC
TAATCCGCGAATGTTCAGAGGTGCAATCCAAGCTCTGGGCCCACTATGCTTTTGGCCAAGAGAAGAACGTGTCTCTGAAC
AATCTGAGTGCTGCTGAGGTGACCAGAGCCATGGAGAATGTGCTAAGCAGCAAAGCTTGA

Alignment

ORF - retro_rnor_262 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAASRVVGAKQVLREIRIHLCQRSPGSQGVRDFIQQRYVELKKAHPDLPILIRECSEVQPKLWARYAFGQ
          AAAS.VVGAK..L.EI.IHLCQRSPGSQG.RDFIQQ.YVELKK.HPDLPILIRECSEVQ.KLWA.YAFGQ
Retrocopy AAASPVVGAKPALHEIHIHLCQRSPGSQGGRDFIQQWYVELKKVHPDLPILIRECSEVQSKLWAHYAFGQ

Parental  EKNVSLNNLSAAEVTKAMENVLSGKA
          EKNVSLNNLSAAEVT.AMENVLS.KA
Retrocopy EKNVSLNNLSAAEVTRAMENVLSSKA

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
SRP017611_brain	0.00 RPM	19.77 RPM
SRP017611_kidney	0.00 RPM	35.80 RPM
SRP017611_liver	0.00 RPM	20.44 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_262 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 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,
Callithrix jacchus	ENSCJAG00000016525	1 retrocopy	retro_cjac_3326,
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,