RetrogeneDB ID: retro_ocun_1712

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018800:468101..468569(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027093
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSOCUG00000008457
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_ocun_1712
ATGGCGGCTCGTGTCCTTTCCTCCTGTGTCCTCCGCCTGTCCGCGGCCTTCTCCCCGCTGCCGCACGTCCCCGCGCTGGC
CTCGGTCCGGCCTCTCGGCACCGTCTTGTGTTCCGCAGGGACCCGGACGAGACTCGGGGCTCTGCAGCCGGCCTCGGTGC
TCGTGCAGGTGCCAGGGAGTGTTACACAGCTGTGCCGCCAGTACAGCGATGCGCCCCCTCTGACACTGGAGGGGATCAGG
GACCACGTTCTTTACGTCTTGAAACTCTACGACAAGATTGACCCAGAGAAGCTCTCGGTAAATTCCCATTTTATGAAAGA
CCTGGGCTTAGACAGTTTGGACCAAGTGGAGATTATCATGGCCATGGAAGACGAATTTGGGTTCGAAATCCCTGATATAG
ATGCAGAAAAGCTAATGTGTCCACAAGAAATAGTAGATTACATTGCAGATAAGAAGGATGTCTATGAA

Alignment

ORF - retro_ocun_1712 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARVLSSCVRRLSAAFSPLPRVPALASVRPLGTVLCSAGTRTRLGALQPASVLVQVPGSVTQLCRQYSD
          MAARVLSSCV.RLSAAFSPLP.VPALASVRPLGTVLCSAGTRTRLGALQPASVLVQVPGSVTQLCRQYSD
Retrocopy MAARVLSSCVLRLSAAFSPLPHVPALASVRPLGTVLCSAGTRTRLGALQPASVLVQVPGSVTQLCRQYSD

Parental  APPLTLEGIRDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMC
          APPLTLEGIRD.VLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMC
Retrocopy APPLTLEGIRDHVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMC

Parental  PQEIVDYIADKKDVYE
          PQEIVDYIADKKDVYE
Retrocopy PQEIVDYIADKKDVYE

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	5.13 RPM	40.56 RPM
SRP017611_kidney	7.60 RPM	59.29 RPM
SRP017611_liver	0.92 RPM	10.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1712 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1712 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Gorilla gorilla	ENSGGOG00000006320	1 retrocopy	retro_ggor_2349,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Oryctolagus cuniculus	ENSOCUG00000008457	1 retrocopy	retro_ocun_1712 ,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,