RetrogeneDB ID: retro_ocun_954

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:68854044..68854330(-)
• Located in intron of: ENSOCUG00000017367

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA38
• Ensembl ID: ENSOCUG00000017359
• Aliases: LOC100358159, LSM8
• Description: N(alpha)-acetyltransferase 38, NatC auxiliary subunit [Source:HGNC Symbol;Acc:20471]

Sequence

>retro_ocun_954
ATGACGTCTGCTTTGGAAAACTACAAAAACTGACCTGTAGCTGTTATTACTTCTGAAGGGCCAGTGACTGTGGGGACACA
GAAAGGCTTTGACCAGACCATTAATCTGATTTTGGATGAAAGCCATGAATGAGTAATTCATCTCCACATAGGGAAAACAA
GTGGTACTGGGGTTGTACCTTGTAAGAGGTGACAATGTTGCACTCATTAAAGAAATTGATGAAGAGACAGATTCAGCACT
TGATTTGGGGAACATTTGAGCAGAACCTCTGAACGCTGTAGCACAC

Alignment

ORF - retro_ocun_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSALENYINRRTVAVITSDGRMIVGTLKGFDQTINLILDESHERV-FSSSQGVEQVVLGLYIVRGDNVA
          MTSALENY.N...VAVITS.G...VGT.KGFDQTINLILDESHE.V.F.S..G..QVVLGLY.VRGDNVA
Retrocopy MTSALENYKN*-PVAVITSEGPVTVGTQKGFDQTINLILDESHE*V>FIST*G-KQVVLGLYLVRGDNVA

Parental  VIGEIDEETDSALDLGNIRAEPLNSVAH
          .I.EIDEETDSALDLGNI.AEPLN.VAH
Retrocopy LIKEIDEETDSALDLGNI*AEPLNAVAH

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	0.11 RPM	13.80 RPM
SRP017611_kidney	0.00 RPM	6.39 RPM
SRP017611_liver	0.00 RPM	2.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_954 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_954 has 0 orthologous retrocopies within eutheria group .

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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,