RetrogeneDB ID: retro_opri_1033

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6059:22294..22549(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA38
• Ensembl ID: ENSOPRG00000014809
• Aliases: None
• Description: N(alpha)-acetyltransferase 38, NatC auxiliary subunit [Source:HGNC Symbol;Acc:20471]

Sequence

>retro_opri_1033
ACAGTCGCTGTGATTACCTCGGATGGGAGAATGATTGTGCGAACACGCAAAGGCTTTGACCAGACCATTAACTTGATTTT
GGACGAAAACCATGAGCCAGTGTTCAGCTCCTCACAGGGAGTAGAACCAGTGGAACTGGGGTTGTACATCGTGAGAGATG
ACAATGTTGCAGCCATTGGAGAAATTGATGAAGAGATGGATTCTGCCCTTGACTTGGGGAACATTCCAGCAGAACCTCAG
AACTCTGTAGCACAC

Alignment

ORF - retro_opri_1033 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQGVEQVVLGLYIVRGDNVAVIGEIDEETDSAL
          TVAVITSDGRMIV.T.KGFDQTINLILDE.HE.VFSSSQGVE.V.LGLYIVR.DNVA.IGEIDEE.DSAL
Retrocopy TVAVITSDGRMIVRTRKGFDQTINLILDENHEPVFSSSQGVEPVELGLYIVRDDNVAAIGEIDEEMDSAL

Parental  DLGNIRAEPLNSVAH
          DLGNI.AEP.NSVAH
Retrocopy DLGNIPAEPQNSVAH

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1033 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001162	1 retrocopy	retro_amel_1716,
Echinops telfairi	ENSETEG00000011594	1 retrocopy	retro_etel_491,
Felis catus	ENSFCAG00000023642	1 retrocopy	retro_fcat_1993,
Myotis lucifugus	ENSMLUG00000006837	1 retrocopy	retro_mluc_161,
Macaca mulatta	ENSMMUG00000015822	1 retrocopy	retro_mmul_2010,
Mustela putorius furo	ENSMPUG00000007100	1 retrocopy	retro_mputfur_1440,
Oryctolagus cuniculus	ENSOCUG00000017359	2 retrocopies	retro_ocun_1715, retro_ocun_954,
Otolemur garnettii	ENSOGAG00000013377	1 retrocopy	retro_ogar_1071,
Ochotona princeps	ENSOPRG00000014809	2 retrocopies	retro_opri_1033 , retro_opri_227,
Sarcophilus harrisii	ENSSHAG00000018435	1 retrocopy	retro_shar_535,
Ictidomys tridecemlineatus	ENSSTOG00000009039	3 retrocopies	retro_itri_1623, retro_itri_364, retro_itri_679,