RetrogeneDB ID: retro_rnor_2178

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:146478798..146479328(+)
• Located in intron of: ENSRNOG00000007629

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prelid1
• Ensembl ID: ENSRNOG00000016410
• Aliases: Prelid1, Preli, RGD1308082
• Description: PRELI domain-containing protein 1, mitochondrial [Source:RefSeq peptide;Acc:NP_001009636]

Sequence

>retro_rnor_2178
GTCTTAACTGAAGACTTAGTGTACCAGGAGGTAACCCCTGACCAGAAGCTTCTGTCCTGGAGACTCCTGACCAAGACCAA
CAGGATGCCACGTTGAGCAGAGTAATTGTTTCCTGCCAATGTCACTCACTCAGTGTATGTCCTGGAGGACTTTAATCTGG
ACCCACAGAATCAGCTCATAATCACCTTCACCCAGAACATCAACCATGCCCAGCTAATGGTGGTGAAGGAATGATGTGTT
TACTGTGTGAACTCTGACAGTAGCAGCTGGACCGGCATCTGTCCGGAAGCCTGGGTCTTTTCTAGCTTATTTGGCATCTC
CAGAGCTTTCCAGGAATTTTTCTTGCCTGTTTCAAAAGAAATGTTACCAAGACAATGGAGGGCTTTGAATATATCCTGCC
CAAGCTACAAGGTAAAGCCCCTTCCAAAACACTTGTTGAGACAACGAAAGAGGCCAAAGAGAAAGCAAAGGAGACAGCAC
AGGCAGCTACAGAGAAGCCCAAGGACCTGGCCAACAAGGCCGCCACCAAG

Alignment

ORF - retro_rnor_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.78 %
• Parental protein coverage: 81.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAERLFPANVAHSVYILEDSIVDPQNQTMTTFTWNINHA
          VLTED.V..EVTPDQKLLS.RLLTKTNRMPR.AE.LFPANV.HSVY.LED...DPQNQ...TFT.NINHA
Retrocopy VLTEDLVYQEVTPDQKLLSWRLLTKTNRMPR*AE*LFPANVTHSVYVLEDFNLDPQNQLIITFTQNINHA

Parental  RLMVVEERCVYCVNSDNSGWTEIRREAWVSSSLFGVSRAVQEF-GLARFKSNVTKTMKGFEYILAKLQGE
          .LMVV.E.CVYCVNSD.S.WT.I..EAWV.SSLFG.SRA.QEF..LA.FK.NVTKTM.GFEYIL.KLQG.
Retrocopy QLMVVKE*CVYCVNSDSSSWTGICPEAWVFSSLFGISRAFQEF<FLACFKRNVTKTMEGFEYILPKLQGK

Parental  APSKTLVETAKEAKEKAKETALAATEKAKDLANKAATK
          APSKTLVET.KEAKEKAKETA.AATEK.KDLANKAATK
Retrocopy APSKTLVETTKEAKEKAKETAQAATEKPKDLANKAATK

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	0.14 RPM	76.28 RPM
SRP017611_kidney	0.00 RPM	141.10 RPM
SRP017611_liver	0.00 RPM	87.48 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2178 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2178 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2394

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002251	1 retrocopy	retro_chof_1025,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401, retro_cjac_3359, retro_cjac_835,
Cavia porcellus	ENSCPOG00000025788	1 retrocopy	retro_cpor_231,
Dasypus novemcinctus	ENSDNOG00000017550	1 retrocopy	retro_dnov_637,
Equus caballus	ENSECAG00000023460	1 retrocopy	retro_ecab_467,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mus musculus	ENSMUSG00000021486	7 retrocopies	retro_mmus_1316, retro_mmus_2079, retro_mmus_2236, retro_mmus_2394, retro_mmus_2672, retro_mmus_449, retro_mmus_866,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Rattus norvegicus	ENSRNOG00000016410	8 retrocopies	retro_rnor_1138, retro_rnor_1166, retro_rnor_1243, retro_rnor_1906, retro_rnor_2178 , retro_rnor_2305, retro_rnor_637, retro_rnor_995,