RetrogeneDB ID: retro_ocun_1395

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:172624199..172624542(-)
• Located in intron of: ENSOCUG00000008565

Retrocopy information

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

Parental gene information

• Parental gene symbol: HYPK
• Ensembl ID: ENSOCUG00000001161
• Aliases: None
• Description: huntingtin interacting protein K (HYPK), mRNA [Source:RefSeq mRNA;Acc:NM_001171256]

Sequence

>retro_ocun_1395
GAGGGGGACGTGGAGCTGGAGTTAGAGACTGAGACCAGCTGCCCAGAGAGGCCTCTTGAGAAGCCACGGAAACCTGACAG
TGGAGCGGCGGACCTGGAGCGGAACTATGCGGAAGAGAAGGAGATCCAGAGTTCCAATCTGTGACGGCCATGTCAGTCAT
TGGAGACAGAAGGTCCCGGGAGCAGAAAGCTAAACAAGAGCGGGAGAAGGAACTGGCTAAAGTCACAATCAAGAAGGAAG
ACTTGGAGCTGATGATGACGAGATGGAGATCTCTCGAGCAGCAGCAGAACGGAGCTTGCGGGAACACATGGACAATGTGG
TCGAGGCTCTTACTGCCCTGACC

Alignment

ORF - retro_ocun_1395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 88.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGDVELELETETSGPERPPEKPRKHDSGAADLERVTDYAEEKEIQSSNL-ETAMSVIGDRRSREQKAKQE
          EGDVELELETETS.PERP.EKPRK.DSGAADLER...YAEEKEIQSSNL..TAMSVIGDRRSREQKAKQE
Retrocopy EGDVELELETETSCPERPLEKPRKPDSGAADLER--NYAEEKEIQSSNL<VTAMSVIGDRRSREQKAKQE

Parental  REKELAKVTIKKEDLELIMT-EMEISRAAAERSLREHMGNVVEALIALT
          REKELAKVTIKKEDLEL.MT.EMEISRAAAERSLREHM.NVVEAL.ALT
Retrocopy REKELAKVTIKKEDLELMMT<EMEISRAAAERSLREHMDNVVEALTALT

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	0.17 RPM	34.44 RPM
SRP017611_kidney	0.00 RPM	21.49 RPM
SRP017611_liver	0.00 RPM	8.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1395 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1395 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002541	2 retrocopies	retro_cjac_1352, retro_cjac_748,
Echinops telfairi	ENSETEG00000007464	3 retrocopies	retro_etel_1504, retro_etel_1616, retro_etel_1830,
Gorilla gorilla	ENSGGOG00000014809	1 retrocopy	retro_ggor_2557,
Macropus eugenii	ENSMEUG00000013059	1 retrocopy	retro_meug_1583,
Monodelphis domestica	ENSMODG00000017744	2 retrocopies	retro_mdom_26, retro_mdom_306,
Nomascus leucogenys	ENSNLEG00000005454	1 retrocopy	retro_nleu_2150,
Oryctolagus cuniculus	ENSOCUG00000001161	2 retrocopies	retro_ocun_1395 , retro_ocun_967,
Otolemur garnettii	ENSOGAG00000010201	1 retrocopy	retro_ogar_1064,
Pongo abelii	ENSPPYG00000006424	1 retrocopy	retro_pabe_3108,
Pan troglodytes	ENSPTRG00000038721	1 retrocopy	retro_ptro_2582,
Rattus norvegicus	ENSRNOG00000015703	1 retrocopy	retro_rnor_2477,
Ictidomys tridecemlineatus	ENSSTOG00000006916	2 retrocopies	retro_itri_1861, retro_itri_1864,
Tursiops truncatus	ENSTTRG00000003726	1 retrocopy	retro_ttru_1499,