RetrogeneDB ID: retro_opri_1044

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_61484:39963..40377(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSOPRG00000014309
• Aliases: None
• Description: N(alpha)-acetyltransferase 50, NatE catalytic subunit [Source:HGNC Symbol;Acc:29533]

Sequence

>retro_opri_1044
AACCAGATCGAGCTGGGAGATGTGACCCCACACAATATTAAACAGTTGAAGAGATTGAACCAAGTCATCTTTCCAGTCAG
TTACAATGACAAGTTCTACAAGGATGTGCTGGAGGTTGGAGAGCTGGAGAAACTTGCCTATTTCAACGACATTGCTGTGG
GTGCAGTGTGCTGTAGGGTGGCTCATTCACAGAATCAGAAGAGGCTGTACATCGTGACACTAGGATGTCTGACACCTTAC
TGAAGGCTAGGAATAGGGACGAAAACATTACATCACGACTTAAACATCTGTGAGAAAGATGGCGCTTTGGACAACATTTA
TCTGCATGTTCAGATCAGCAATGAGTCGGCAATTGATTTCTACAGGAAGTTTGGCTTTGAGATTATTGAGACAAAGAACT
ACTATAACAGGATA

Alignment

ORF - retro_opri_1044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 83.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLY
          ..IELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGEL.KLAYFNDIAVGAVCCRV.HSQNQKRLY
Retrocopy NQIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELEKLAYFNDIAVGAVCCRVAHSQNQKRLY

Parental  IMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRI
          I.TLGCL.PY.RLGIGTK.L.H.LNICEKDG..DNIYLHVQISNESAIDFYRKFGFEIIET.KNYY.RI
Retrocopy IVTLGCLTPY*RLGIGTKTLHHDLNICEKDGALDNIYLHVQISNESAIDFYRKFGFEIIET-KNYYNRI

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_1044 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018160	1 retrocopy	retro_mdom_1645,
Otolemur garnettii	ENSOGAG00000011197	1 retrocopy	retro_ogar_157,
Ochotona princeps	ENSOPRG00000014309	1 retrocopy	retro_opri_1044 ,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,