RetrogeneDB ID: retro_btau_124

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:64586966..64587266(-)
• Located in intron of: ENSBTAG00000018035

Retrocopy information

• Ensembl ID: ENSBTAG00000047836
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NDUFA2
• Ensembl ID: ENSBTAG00000015041
• Aliases: NDUFA2, B8, CI-B8
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q02370]

Sequence

>retro_btau_124
ATGGCGGCGGCTGCAGCGATTCGTGGGGTCCGAGGCAAATTGGGTCTTCGTGAAATTCGTATCCATTTGTGCCAGCGCTG
GCCCGGCAGCCAGGGCGTCAGGGACTTCATTGAGAAACGCTATGTGGAGCTGAAGAAAGCGAATCCCGACCTGCCCATCC
TAATCTGCAAGTGCTCGGATGTGCAGCCCAAGCTCTGGGCCCGCTACGCATTTGGCCAAGAGAAGAATGTCTCTCTGAAC
AACTTCAGTGCTGATCAGGTAACTAGAGCCCTGGAGAATGTGCTAAGTAGCAAAGCCTGA

Alignment

ORF - retro_btau_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAAIRGVRGKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYA
          MAAAAAIRGVRGKLGLREIRIHLCQR.PGSQGVRDFIEKRYVELKKANPDLPILI..CSDVQPKLWARYA
Retrocopy MAAAAAIRGVRGKLGLREIRIHLCQRWPGSQGVRDFIEKRYVELKKANPDLPILICKCSDVQPKLWARYA

Parental  FGQEKNVSLNNFSADQVTRALENVLSSKA
          FGQEKNVSLNNFSADQVTRALENVLSSKA
Retrocopy FGQEKNVSLNNFSADQVTRALENVLSSKA

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
ERP005899_liver	0.00 RPM	24.15 RPM
ERP005899_muscle	0.21 RPM	45.29 RPM
SRP017611_brain	0.00 RPM	18.96 RPM
SRP017611_kidney	0.06 RPM	30.58 RPM
SRP017611_liver	0.00 RPM	19.63 RPM
SRP030211_testis	0.03 RPM	19.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_124 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_124 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,