RetrogeneDB ID: retro_ocun_1143

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:20023919..20024461(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM40
• Ensembl ID: ENSOCUG00000023582
• Aliases: None
• Description: translocase of outer mitochondrial membrane 40 homolog (yeast) [Source:HGNC Symbol;Acc:18001]

Sequence

>retro_ocun_1143
GGTCCTGGAGGCCAGGTCCAGCACAGGTCAAGGTTCAGAATGGATCTCAGGGTGTCTGCTGATAGCAATGCATGGCCCTC
TGAAGGTGAGGGTGGCAGCTTCCTGCCCAAACTTTACAGGTTGGAGGAGTGCCACTGAAAGTGCCCAGATTTGTTTCCAT
TCAGATGTCAGGTGTCAAATTCAAAGTCAACAAAGAGCTTAATCATTTCCAGGTGAACTACACAGTAGACCTCACCAGGG
AGTCCAACTACCATTTCAGGGTTACCTACATGGGGGCAAAGGCAGCCGATTCCACTGAGGCATTCCTGTCTGTTGGTGCT
GGCCCACACAGCCAACAACAGGCTCCATGCTCAAGTCATTCAGGTGGGGTCCAGCCTCATTTATTTGGCCATCCAGAACC
AGCAGCCAAAGTTTCTGAACTGGCAGGTGGACAGGGGTACCAAGGCTCTAATTTCATAGTGGCCATCACCCTGAAGAACC
TAGACAACCTGCTTGTGTCAAGAATCCTCATGGCCCACCTCCTGCAAAGCATCACTGGGTCT

Alignment

ORF - retro_ocun_1143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.26 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GGGSLGSGRMAGRGSERTAGASAAGVADDGACGCLPNPGTFEECHRKCKELFP-IQMEGVKLTVNKGLSN
          G.G.....R...R...R....S.A..........LP.....EECH.KC..LFP.IQM.GVK..VNK.L.N
Retrocopy GPGGQVQHRSRFRMDLRVSADSNAWPSEGEGGSFLPKLYRLEECH*KCPDLFP<IQMSGVKFKVNKEL-N

Parental  HFQVNHTVALSTVGESNYHFGVTYVGTKQLSPTEAFP-VLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQT
          HFQVN.TV.L....ESNYHF.VTY.G.K....TEAF...LV........L.AQVI.Q.G..L....AIQ.
Retrocopy HFQVNYTVDLTR--ESNYHFRVTYMGAKAADSTEAFL>LLVLAHTANNRLHAQVI-QVGSSL-IYLAIQN

Parental  QQSKFVNWQVDGE-YRGSDFTAAVTLGNPDVLVGSGILVAHYLQSITPS
          QQ.KF.NWQVD...Y.GS.F..A.TL.N.D.L..S.IL.AH.LQSIT.S
Retrocopy QQPKFLNWQVDRG<YQGSNFIVAITLKNLDNLLVSRILMAHLLQSITGS

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	23.68 RPM
SRP017611_kidney	0.00 RPM	18.45 RPM
SRP017611_liver	0.00 RPM	4.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1143 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130204	5 retrocopies	retro_hsap_1300, retro_hsap_1386, retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143 ,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,