RetrogeneDB ID: retro_rnor_1596

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:282732039..282732678(+)
• Located in intron of: ENSRNOG00000010325

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vdac3
• Ensembl ID: ENSRNOG00000019277
• Aliases: None
• Description: Voltage-dependent anion-selective channel protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9R1Z0]

Sequence

>retro_rnor_1596
GGGCTCACCTTCACCCAAACGTGGAATACAGACAATATTCTCTGGACAGAAATCTCTTGAGAGAATAAGTTGGCTGAAGG
GTTGAAACTGACTCTTGATATCATATTTGCACCAAACACAGGGAAAAAAGAGTGGGAAATTAAAGGCCTCCTATAAACGG
GATTGTTTTAGTCTGGGCAGTAATGTTGATATAGATTTTTCGGGACCGACAATTCATGGCTTGGTTGTGTTGGCCTTTGA
AGGTTGGCTTGCCAGCTATCAGATAAGTTTTGACACAGCCAAATCCAAAGTGTCTCAGAACAATTTTGCTCTTGGTTACA
AGGCTGCAGACCTGTGCACTCATGTGAACAATGGCACTGAATTTAGAGGCTCTATCTACCAGAAAGTTAACAAGATCAAA
ATGTGAATAAACCTAGCGTGAACAGCTGTCAGCAACAACACTCATTTTGGCATTGCTACTAAATATAAGCTGGATCACAG
AACTTCTCTATCTGCCAGAGTAAATAATGCCAGATTAATTGGACTGGGTTATATGCAGACCCTCCAACCAGGAGTCAAAC
TGACCATGTCAGTTTTAATAGATGGAAAGAACTTCGATGTACGAGGTCACAAGGTCGGATTGGGGTTGAACTGGAAGCT

Alignment

ORF - retro_rnor_1596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.98 %
• Parental protein coverage: 76.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLIFTQKWNTDNTLGTEISWENKLAEGLKLTVDTIFVPNTGKK-SGKLKASYRRDCFSVGSNVDIDFSGP
          GL.FTQ.WNTDN.L.TEIS.ENKLAEGLKLT.D.IF.PNTGKK.SGKLKASY.RDCFS.GSNVDIDFSGP
Retrocopy GLTFTQTWNTDNILWTEIS*ENKLAEGLKLTLDIIFAPNTGKK>SGKLKASYKRDCFSLGSNVDIDFSGP

Parental  TIYGWAVLAFEGWLAGYQMSFDTAKSKLCQNNFALGYKAEDFQLHTHVNDGTEFGGSIYQRVNEKIETSI
          TI.G..VLAFEGWLA.YQ.SFDTAKSK..QNNFALGYKA.D..L.THVN.GTEF.GSIYQ.VN.KI...I
Retrocopy TIHGLVVLAFEGWLASYQISFDTAKSKVSQNNFALGYKAAD--LCTHVNNGTEFRGSIYQKVN-KIKM*I

Parental  NLAWTAGSNNTRFGIAAKYRLDCRTSLSAKVNNASLIGLGYTQSLRPGVKLTLSALVDGKNFNAGGHKVG
          NLA.TA.SNNT.FGIA.KY.LD.RTSLSA.VNNA.LIGLGY.Q.L.PGVKLT.S.L.DGKNF...GHKVG
Retrocopy NLA*TAVSNNTHFGIATKYKLDHRTSLSARVNNARLIGLGYMQTLQPGVKLTMSVLIDGKNFDVRGHKVG

Parental  LGF-ELEA
          LG..ELEA
Retrocopy LGL<ELEA

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	131.86 RPM
SRP017611_kidney	0.00 RPM	111.86 RPM
SRP017611_liver	0.00 RPM	53.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1596 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 60 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907,
Rattus norvegicus	ENSRNOG00000006375	8 retrocopies	retro_rnor_1235, retro_rnor_1398, retro_rnor_1482, retro_rnor_1594, retro_rnor_1664, retro_rnor_776, retro_rnor_777, retro_rnor_947,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596 ,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,