RetrogeneDB ID: retro_ocun_466

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:30720994..30721483(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000089
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSOCUG00000006467
• Aliases: None
• Description: N(alpha)-acetyltransferase 50, NatE catalytic subunit [Source:HGNC Symbol;Acc:29533]

Sequence

>retro_ocun_466
AGCCGGATCGAGCTGGGAGATGTGACACCACACAATATTAAACAGTTGAAGAGGTTGAACCAAGTTATCTTTCCAGTCAG
CTACAATGACAAGTTCTACAAGGACGCGCTGGAGGTTGGAGAGCTAGCAAAAACTGCCTATTTCAATGATATTTGCTATA
GGTGCAGTATGCTGTAGGGGGATCATCACAGGATCAGAGAGGCGTTACATCATGACACTAGGATGTCTGGCACCTTACCG
AAGGCCTAGGAATAGGGACGAAAATGCTAAATCACTCTTAAACATCTGTGAAAAAGATGAAGCTTTGACATTTATCTGCA
TGTGCAGATCAGCAATGAATCGGCAATTAACTTCTACAGGAAATTTGGCATTGAGATTATTGAGACAAAGAACTACTGTA
AGAGGATAGAGCAAGCAGATGATCACGTGCTACAGAAAAACCTCAAAGTCCCTTCCAGTCAGAATGCAGACGTGCAAAAG
ACAGACAAC

Alignment

ORF - retro_ocun_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.12 %
• Parental protein coverage: 98.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDI-AVGAVCCRVDHSQNQKRL
          SRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKD.LEVGELAK.AYFNDI.A.GAVCCR........R.
Retrocopy SRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDALEVGELAKTAYFNDI>AIGAVCCRGIITGSERR-

Parental  YIMTLGCLAPYRR-LGIGTKMLNH-VLNICEKDG-TFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYY
          YIMTLGCLAPYRR.LGIGTKMLNH..LNICEKD...FD.IYLHVQISNESAI.FYRKFG.EIIET.KNY.
Retrocopy YIMTLGCLAPYRR>LGIGTKMLNH<LLNICEKDE<SFD-IYLHVQISNESAINFYRKFGIEIIET-KNYC

Parental  KRIEPADAHVLQKNLKVPSGQNADVQKTDN
          KRIE.AD.HVLQKNLKVPS.QNADVQKTDN
Retrocopy KRIEQADDHVLQKNLKVPSSQNADVQKTDN

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	29.25 RPM
SRP017611_kidney	0.10 RPM	30.41 RPM
SRP017611_liver	0.00 RPM	10.64 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_466 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014169	6 retrocopies	retro_cpor_1027, retro_cpor_1028, retro_cpor_1199, retro_cpor_1200, retro_cpor_217, retro_cpor_480,
Gorilla gorilla	ENSGGOG00000006589	2 retrocopies	retro_ggor_432, retro_ggor_710,
Loxodonta africana	ENSLAFG00000004023	1 retrocopy	retro_lafr_1159,
Oryctolagus cuniculus	ENSOCUG00000006467	2 retrocopies	retro_ocun_466 , retro_ocun_984,
Otolemur garnettii	ENSOGAG00000011197	1 retrocopy	retro_ogar_157,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,