RetrogeneDB ID: retro_rnor_272

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:101150579..101151107(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004791
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Arf3
• Ensembl ID: ENSRNOG00000033155
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:UniProtKB/Swiss-Prot;Acc:P61206]

Sequence

>retro_rnor_272
ATGGGGAAGGTGCTATCCAAGATCTTCGGGAACAAGGAAATGCGGATCCTCATGCTGGGCCTGGACGCAGCCGGCAAGAC
AACGATCCTGTACAAGTTGAAGCTGGGCCAGTCTGTGACCACCATTCCCACGGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAACGTCAAGTTCAACGTGTGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACCGGG
ACCCAGGGTCTGATCTTCGTGGTAGACTGCGCCGACCGCGACCGCATCGATGAGGCCCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCTGATGCCATGAAACCCCATG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCCGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCCTAA

Alignment

ORF - retro_rnor_272 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 96.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
          G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
Retrocopy GKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR

Parental  PLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
          PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
Retrocopy PLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL

Parental  HSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
          ...R.RNWY.Q..CATSGDGLYEGL.WL....K.
Retrocopy TRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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	12.51 RPM	89.22 RPM
SRP017611_kidney	21.35 RPM	10.33 RPM
SRP017611_liver	19.10 RPM	3.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_272 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_272 has 12 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_36
Pan troglodytes	retro_ptro_5
Gorilla gorilla	retro_ggor_161
Pongo abelii	retro_pabe_126
Macaca mulatta	retro_mmul_174
Callithrix jacchus	retro_cjac_300
Mus musculus	retro_mmus_147
Oryctolagus cuniculus	retro_ocun_132
Bos taurus	retro_btau_26
Sus scrofa	retro_sscr_82
Canis familiaris	retro_cfam_119
Equus caballus	retro_ecab_106

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008240	1 retrocopy	retro_acar_12,
Ailuropoda melanoleuca	ENSAMEG00000007042	2 retrocopies	retro_amel_28, retro_amel_70,
Canis familiaris	ENSCAFG00000008767	1 retrocopy	retro_cfam_119,
Cavia porcellus	ENSCPOG00000025074	1 retrocopy	retro_cpor_92,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000000088	2 retrocopies	retro_fcat_2, retro_fcat_59,
Homo sapiens	ENSG00000134287	1 retrocopy	retro_hsap_36,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Loxodonta africana	ENSLAFG00000004207	1 retrocopy	retro_lafr_115,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus	ENSMICG00000017545	1 retrocopy	retro_mmur_37,
Myotis lucifugus	ENSMLUG00000029846	1 retrocopy	retro_mluc_119,
Macaca mulatta	ENSMMUG00000006968	1 retrocopy	retro_mmul_174,
Monodelphis domestica	ENSMODG00000013804	1 retrocopy	retro_mdom_241,
Mustela putorius furo	ENSMPUG00000014730	1 retrocopy	retro_mputfur_86,
Mus musculus	ENSMUSG00000051853	1 retrocopy	retro_mmus_147,
Nomascus leucogenys	ENSNLEG00000017859	2 retrocopies	retro_nleu_1348, retro_nleu_94,
Ochotona princeps	ENSOPRG00000007411	2 retrocopies	retro_opri_13, retro_opri_3,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Pongo abelii	ENSPPYG00000004473	1 retrocopy	retro_pabe_126,
Pteropus vampyrus	ENSPVAG00000004626	1 retrocopy	retro_pvam_7,
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,
Sarcophilus harrisii	ENSSHAG00000003635	2 retrocopies	retro_shar_25, retro_shar_364,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000004698	1 retrocopy	retro_ttru_1081,