RetrogeneDB ID: retro_ocun_1335

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:153002500..153002942(+)
• Located in intron of: ENSOCUG00000009790

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B12
• Ensembl ID: ENSOCUG00000016351
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 12 [Source:HGNC Symbol;Acc:18646]

Sequence

>retro_ocun_1335
AAAAAATTCAAAGTAGAAACAAGAACTATTCTTGTTGAATTTACATCAGAAGATATTTATGATAAAATTGAAATAGAGTT
TGCAGTTCTTGAAATTGTCATTTTTAGTGAAAAATGTGGGAAAATCATCTGAGTACACTGAATACATTTTGGACATTCCT
GACTTGGACAACAGCATCAAGAAACGGCTAAATATTGTTCTTGTTTGTAAGACGACCTGATTGCTGCTGACTCACATGGT
CGAAAGATGTAGAGGCATCATTCTAAGTATCGCCATCGCCAACGGCATGATCCCAGTTCTGCTACTGAGCATCTACTTGG
GAACGGAGACTTACATAGATTTCTTCTCTCAAAGCCTCCCTGAGGCTTACAGGAGCAAGAGCATCTTTGTGCAGAACATC
CTGACATATTTTGCCACTTGTAAATTCAGAGATATTTGTAAA

Alignment

ORF - retro_ocun_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.67 %
• Parental protein coverage: 52.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKFKVETRTIAVDFASEDIYNKIETGLAGLEIGV-LVNNVGMSYEYPEYFLDIPDLDNTIKKLININVLS
          .KFKVETRTI.V.F.SEDIY.KIE...A.LEI...LV.NVG.S.EY.EY.LDIPDLDN.IKK....N...
Retrocopy KKFKVETRTILVEFTSEDIYDKIEIEFAVLEIVI>LVKNVGKSSEYTEYILDIPDLDNSIKK--RLNIVL

Parental  VCKMTRLVLPRMVERSKGAILNISSASGTFPVPLLTIYSATKAFVDFFSQCLHEEYRSKGIFVQSVLPYY
          VCK.T.L.L..MVER..G.IL.I..A.G..PV.LL.IY..T....DFFSQ.L.E.YRSK.IFVQ..L.Y.
Retrocopy VCKTT*LLLTHMVERCRGIILSIAIANGMIPVLLLSIYLGTETYIDFFSQSLPEAYRSKSIFVQNILTYF

Parental  VATKLAKIRK
          ...K...I.K
Retrocopy ATCKFRDICK

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	29.19 RPM
SRP017611_kidney	0.00 RPM	32.33 RPM
SRP017611_liver	0.00 RPM	14.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1335 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1335 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1335 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011325	1 retrocopy	retro_cjac_2489,
Dipodomys ordii	ENSDORG00000004834	1 retrocopy	retro_dord_561,
Homo sapiens	ENSG00000149084	1 retrocopy	retro_hsap_3684,
Gorilla gorilla	ENSGGOG00000002003	1 retrocopy	retro_ggor_2491,
Nomascus leucogenys	ENSNLEG00000017959	1 retrocopy	retro_nleu_2273,
Oryctolagus cuniculus	ENSOCUG00000016351	1 retrocopy	retro_ocun_1335 ,
Otolemur garnettii	ENSOGAG00000009102	1 retrocopy	retro_ogar_3391,
Pongo abelii	ENSPPYG00000003343	1 retrocopy	retro_pabe_3021,
Pan troglodytes	ENSPTRG00000003522	1 retrocopy	retro_ptro_2499,
Ictidomys tridecemlineatus	ENSSTOG00000005473	1 retrocopy	retro_itri_1099,
Tursiops truncatus	ENSTTRG00000005103	1 retrocopy	retro_ttru_772,