RetrogeneDB ID: retro_rnor_1884

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:51342312..51342768(-)
• Located in intron of: ENSRNOG00000031951

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arf4
• Ensembl ID: ENSRNOG00000012623
• Aliases: None
• Description: ADP-ribosylation factor 4 [Source:UniProtKB/Swiss-Prot;Acc:P61751]

Sequence

>retro_rnor_1884
TCTTCTCTCTCCTTGAGCATCTTCTGCAAGAAGCAGATGCACATGTTGATGGTTGAATTGGATGCTGCGGGGAAGATGAC
AATTCTGTATAAATTGAAATAGGGGAGATAGTCACCACCATTCCTACCATTGGTTTTAATGTGGGAACAGTAGAATATAA
GAGCATTTGTTTCACAGTATAGGATATTGGTGGTCAAGATAAAATTAGGCCTCTCTGGAGGCATTACTTCCAGAATACCC
AGGGTCTCATTTTCGTGGTTGATAGCAATGATGTGAAAGAATTTCAGGAAGGAGTGCAGAAAATGCTTCTGGCAGATGAG
CTGCAGGACACTGTGCTGCTGCTTTTTACAAACACAGGATTTGCCAAATGCTATGGCCATCAGTGAGATGACGGATAAGT
TAGGTCTTCAGTCTGTCCGCAACACCACATGGTATGTCTAAGCCACTTGTGCTACA

Alignment

ORF - retro_rnor_1884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.11 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSLFSRLFGKKQMRILMVGLDAAGKTTILYKLK-LGEIVTTIPTIGFNVETVEYKNICFTVWDVGGQDKI
          SSL....F.KKQM..LMV.LDAAGK.TILYKLK..GEIVTTIPTIGFNV.TVEYK.ICFTV.D.GGQDKI
Retrocopy SSLSLSIFCKKQMHMLMVELDAAGKMTILYKLK<IGEIVTTIPTIGFNVGTVEYKSICFTV*DIGGQDKI

Parental  RPLWRHYFQNTQGLIFVVDSNDRERIQEGAAVLQKMLLEDELQDAVLLL-FANKQDLPNAMAISEMTDKL
          RPLWRHYFQNTQGLIFVVDSND....QEG....QKMLL.DELQD.V.LL.F...QDLPNAMAISEMTDKL
Retrocopy RPLWRHYFQNTQGLIFVVDSNDVKEFQEG---VQKMLLADELQDTV-LL>FLQTQDLPNAMAISEMTDKL

Parental  GLQSLRNRTWYVQATCAT
          GLQS.RN.TWYV.ATCAT
Retrocopy GLQSVRNTTWYV*ATCAT

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	60.82 RPM
SRP017611_kidney	0.00 RPM	155.96 RPM
SRP017611_liver	0.00 RPM	74.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1884 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016069	1 retrocopy	retro_btau_542,
Choloepus hoffmanni	ENSCHOG00000006427	4 retrocopies	retro_chof_1024, retro_chof_1807, retro_chof_2368, retro_chof_36,
Ciona intestinalis	ENSCING00000021790	1 retrocopy	retro_cint_10,
Callithrix jacchus	ENSCJAG00000019922	1 retrocopy	retro_cjac_507,
Cavia porcellus	ENSCPOG00000010334	1 retrocopy	retro_cpor_1261,
Dipodomys ordii	ENSDORG00000004312	1 retrocopy	retro_dord_731,
Homo sapiens	ENSG00000168374	2 retrocopies	retro_hsap_1296, retro_hsap_4221,
Gorilla gorilla	ENSGGOG00000000294	1 retrocopy	retro_ggor_1552,
Microcebus murinus	ENSMICG00000002015	3 retrocopies	retro_mmur_1528, retro_mmur_1558, retro_mmur_360,
Myotis lucifugus	ENSMLUG00000007990	1 retrocopy	retro_mluc_2272,
Macaca mulatta	ENSMMUG00000018617	1 retrocopy	retro_mmul_50,
Monodelphis domestica	ENSMODG00000000185	1 retrocopy	retro_mdom_1538,
Nomascus leucogenys	ENSNLEG00000007270	3 retrocopies	retro_nleu_2106, retro_nleu_2703, retro_nleu_2704,
Oryctolagus cuniculus	ENSOCUG00000000824	4 retrocopies	retro_ocun_1007, retro_ocun_1502, retro_ocun_1868, retro_ocun_987,
Otolemur garnettii	ENSOGAG00000012034	4 retrocopies	retro_ogar_1407, retro_ogar_1501, retro_ogar_2963, retro_ogar_764,
Pongo abelii	ENSPPYG00000013768	3 retrocopies	retro_pabe_1013, retro_pabe_1075, retro_pabe_3451,
Pan troglodytes	ENSPTRG00000015051	2 retrocopies	retro_ptro_2866, retro_ptro_888,
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,
Sorex araneus	ENSSARG00000009272	1 retrocopy	retro_sara_681,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614,
Tupaia belangeri	ENSTBEG00000007415	1 retrocopy	retro_tbel_2075,
Tarsius syrichta	ENSTSYG00000009748	1 retrocopy	retro_tsyr_2059,
Tursiops truncatus	ENSTTRG00000015381	1 retrocopy	retro_ttru_284,
Vicugna pacos	ENSVPAG00000003891	1 retrocopy	retro_vpac_459,