RetrogeneDB ID: retro_ocun_1636

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018733:2158564..2158914(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT4H1
• Ensembl ID: ENSOCUG00000025823
• Aliases: None
• Description: suppressor of Ty 4 homolog 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:11467]

Sequence

>retro_ocun_1636
ATGGCTCTGGAGACTGTATTGTAGGACCTGTGGCATCCACGGGCTTGTTTGCTGGGTTCGCTGGTCAAGACTATAGACCA
GATTGAATACGGCAGTTGTGACCATGGTGATGCGTACCTACAGATGAGGGGTAACCGAGGGGCAGCATATGACTGCACCT
GCTCTTCCTTTCATGGAACTATTGCCATGATGCATCCAGAAGACAGTTGGGTCTCCAAGTGGCCACGAGTCAGCAACTTT
AAGCCAGGTATGGATGCGGTGTCAGTCACTGGTCACCTGCCACAGGAATCGTGTGGGAGCTGAAAAGCCGAGGAGCAGCC
TACACATCCAGAGACACAGTTATAAAGACT

Alignment

ORF - retro_ocun_1636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSW
          MALETV..DL.H.RACLL.SLVKTIDQ.EY..CD..DAYLQM.GNR...YDCT.SSF.G.IAMM.PEDSW
Retrocopy MALETVL*DLWHPRACLLGSLVKTIDQIEYGSCDHGDAYLQMRGNRGAAYDCTCSSFHGTIAMMHPEDSW

Parental  VSKWQRVSNFKPGVYAVSVTGRLPQ-GIVRELKSRGVAYKSRDTAIKT
          VSKW.RVSNFKPG..AVSVTG.LPQ.GIV.ELKSRG.AY.SRDT.IKT
Retrocopy VSKWPRVSNFKPGMDAVSVTGHLPQ<GIVWELKSRGAAYTSRDTVIKT

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	27.65 RPM
SRP017611_kidney	0.00 RPM	35.98 RPM
SRP017611_liver	0.00 RPM	7.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1636 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1636 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017524	2 retrocopies	retro_cfam_1399, retro_cfam_553,
Homo sapiens	ENSG00000213246	2 retrocopies	retro_hsap_1081, retro_hsap_2280,
Gorilla gorilla	ENSGGOG00000007232	2 retrocopies	retro_ggor_1693, retro_ggor_854,
Macropus eugenii	ENSMEUG00000010164	1 retrocopy	retro_meug_2079,
Myotis lucifugus	ENSMLUG00000025583	1 retrocopy	retro_mluc_761,
Macaca mulatta	ENSMMUG00000007579	2 retrocopies	retro_mmul_1005, retro_mmul_842,
Mus musculus	ENSMUSG00000020485	2 retrocopies	retro_mmus_2857, retro_mmus_633,
Nomascus leucogenys	ENSNLEG00000008159	3 retrocopies	retro_nleu_1619, retro_nleu_1962, retro_nleu_2714,
Oryctolagus cuniculus	ENSOCUG00000025823	2 retrocopies	retro_ocun_1613, retro_ocun_1636 ,
Pongo abelii	ENSPPYG00000008233	1 retrocopy	retro_pabe_1940,
Pan troglodytes	ENSPTRG00000009451	2 retrocopies	retro_ptro_1614, retro_ptro_735,
Pteropus vampyrus	ENSPVAG00000002320	1 retrocopy	retro_pvam_477,
Rattus norvegicus	ENSRNOG00000007845	3 retrocopies	retro_rnor_1255, retro_rnor_1973, retro_rnor_556,