RetrogeneDB ID: retro_pabe_938

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:71170592..71170889(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA2
• Ensembl ID: ENSPPYG00000015860
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:P0CB79]

Sequence

>retro_pabe_938
ATGGCGGCGGCCGCAGCGAGTCGAGGAATCAGGGCAAAGCTGGGCCTGCGTGAGATTCGCATCCACTTATGTCAGCGCTC
GTCCGGCAGCCAGGGTGTCAGGGACTTCATTGAGAAACGCTACGTGGAGCGGAAGAAGGCGAATGCCGACCTACCCATCC
TAATCCGCGAATGCTACGATGTGCAGCCCAAGCTCTGGGCCTGCTACGCATTTGGCCAAGAGAAGAATGTCCGTTTGTAC
AACTGCAGTGCTGATCAGGTAACCAGAGCCCCGGAGAACGTGCTAAGTGGTAAAGCC

Alignment

ORF - retro_pabe_938 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.87 %
• Parental protein coverage: 96.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAASRGIGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYA
          MAAAAASRGI.AKLGLREIRIHLCQRS.GSQGVRDFIEKRYVE.KKAN.DLPILIREC.DVQPKLWA.YA
Retrocopy MAAAAASRGIRAKLGLREIRIHLCQRSSGSQGVRDFIEKRYVERKKANADLPILIRECYDVQPKLWACYA

Parental  FGQEKNVPLNNFSADQVTRALENVLKPEA
          FGQEKNV.L.N.SADQVTRA.ENVL...A
Retrocopy FGQEKNVRLYNCSADQVTRAPENVLSGKA

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	29.80 RPM
SRP007412_cerebellum	0.00 RPM	28.58 RPM
SRP007412_heart	0.00 RPM	58.07 RPM
SRP007412_kidney	0.00 RPM	64.07 RPM
SRP007412_liver	0.00 RPM	46.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_938 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_938 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,