RetrogeneDB ID: retro_rnor_1348

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:40547599..40547882(+)
• Located in intron of: ENSRNOG00000003950

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arf1
• Ensembl ID: ENSRNOG00000030591
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:RefSeq peptide;Acc:NP_071963]

Sequence

>retro_rnor_1348
ATGGGGAATAGCTTTAAAAACCTCTTCAAGGGCCGATTCAGCAAAATAGAAGTGTGCGTTCCCACGGTGGCCCTGGATGC
TACACGAGGACAACTCTATACCAACTGAAGTTAGGCAACATTGTGACCACAACTCCTACCATTGATTTCAACGTGGAGAC
CACTGAGTACAAGAACCTCAGCTTCATTGTGTGGGATGCAGGAGGCCAGGACAAGGTCCACCACTTCTTCCAGAACACCC
AAGGCTTGATCTTCAAAATGATGGCAAAGACAGAGAGCGTGTG

Alignment

ORF - retro_rnor_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.71 %
• Parental protein coverage: 55.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAA-GKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVG
          MGN.F.NLFKG.F.K.E.....V.LDA....TT.LY.LKLG.IVTT.PTI.FNVET.EYKN.SF.VWD.G
Retrocopy MGNSFKNLFKGRFSKIEVCVPTVALDAT<TRTT-LYQLKLGNIVTTTPTIDFNVETTEYKNLSFIVWDAG

Parental  GQDKIRPLWRHYFQNTQGLIFVV-DSNDRERV
          GQDK......H.FQNTQGLIF...D..DRERV
Retrocopy GQDKV----HHFFQNTQGLIFKM<DGKDRERV

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	281.04 RPM
SRP017611_kidney	0.00 RPM	278.71 RPM
SRP017611_liver	0.00 RPM	162.65 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1348 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1348 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1718

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Nomascus leucogenys	ENSNLEG00000014137	3 retrocopies	retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Ochotona princeps	ENSOPRG00000015063	2 retrocopies	retro_opri_317, retro_opri_759,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pteropus vampyrus	ENSPVAG00000007383	1 retrocopy	retro_pvam_1324,
Rattus norvegicus	ENSRNOG00000012623	2 retrocopies	retro_rnor_1036, retro_rnor_1884,
Rattus norvegicus	ENSRNOG00000030591	3 retrocopies	retro_rnor_1268, retro_rnor_1348 , retro_rnor_1950,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Sus scrofa	ENSSSCG00000013992	2 retrocopies	retro_sscr_429, retro_sscr_82,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,