RetrogeneDB ID: retro_tbel_2688

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_116647:213229..213528(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA2
• Ensembl ID: ENSTBEG00000005978
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7685]

Sequence

>retro_tbel_2688
GCAGTGGCTGCAGCAACTCATGGGGTCGTGGTTGCAAAGCTTGCCTTGCGTAAGATTCACATCCACTTACGCCAGTGCTC
ACCAGGCAACCAGGGTATGAGGGACTTCATTGACAAGTGCTATGTAGAGCTGATGAAGATGAGCCCCAACTTTACCTATC
CTGAACCAAGAATGCGCCGATGTGCAGCCCAAACTCTGGGCTTGCTACCCATTTGACCAAGAGAAGGACATCACTTTAAG
CAGCCTCAGTGCTGACCAGGTAACCTGAGCACGTGGAGAATGTGCTAAGTAGCAAAGCC

Alignment

ORF - retro_tbel_2688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.32 %
• Parental protein coverage: 99.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAAAASRGVAAAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPD-LPILIRECSDVQPKLWARY
          A.AAA..GV..AKL.LR.I.IHL.Q.SPG.QG.RDFI.K.YVEL.K..P..LPIL..EC.DVQPKLWA.Y
Retrocopy AVAAATHGVVVAKLALRKIHIHLRQCSPGNQGMRDFIDKCYVELMKMSPN>LPILNQECADVQPKLWACY

Parental  AFGQEKNITLNNLSADQVTRA-LENVLSGKA
          .F.QEK.ITL..LSADQVT.A..ENVLS.KA
Retrocopy PFDQEKDITLSSLSADQVT*A>VENVLSSKA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2688 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2688 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 ,