RetrogeneDB ID: retro_cpor_1045

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_40:17888536..17888804(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA2
• Ensembl ID: ENSCPOG00000009178
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 [Source:UniProtKB/TrEMBL;Acc:H0VE12]

Sequence

>retro_cpor_1045
ATGGTGCTGATCATGGCCAGTAGAGCCTCCCAAGCAGAGCTGGGCATACAGGAAATTCAGACTCACACTCATGCCAGCAC
TTGAGGGCATCAGGGACTTCATCAAGAAATGCTAAGTGGAACTGAAGAAAGCAAACCTAGGCCTGATCAATCTAATCCAC
AAATGCTCTGTGGTGCAGCTCAAGCCCTTGGCCCACTAAGCATTTCGCCAAGGGAAGAATGTCTCTTTGAGCCACTTCAG
TGCTGATCAGGTAATCAGAGGTCTGAAG

Alignment

ORF - retro_cpor_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.69 %
• Parental protein coverage: 92.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAAASRVVGAKLGL-REIRIHLCQRSPGSQGVRDFIQKRYVELKKANPDLPILIRECSDVQPKLWARY
          M....ASR...A.LG..R..R..L....P...G.RDFI.K..VELKKAN..L..LI..CS.VQ.K..A..
Retrocopy MVLIMASRASQAELGI>RKFRLTLM---PALEGIRDFIKKC*VELKKANLGLINLIHKCSVVQLKPLAH*

Parental  AFGQEKNVSLNNFSADQVTRALE
          AF.Q.KNVSL..FSADQV.R.L.
Retrocopy AFRQGKNVSLSHFSADQVIRGLK

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	15.53 RPM
SRP017611_kidney	0.00 RPM	34.86 RPM
SRP017611_liver	0.00 RPM	29.47 RPM
SRP040447_lung	0.03 RPM	19.92 RPM
SRP040447_skeletal_muscle	0.03 RPM	49.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1045 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1045 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,