RetrogeneDB ID: retro_rnor_458

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:87832558..87833051(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Polr3g
• Ensembl ID: ENSRNOG00000016260
• Aliases: None
• Description: DNA-directed RNA polymerase III subunit RPC7 [Source:RefSeq peptide;Acc:NP_001102938]

Sequence

>retro_rnor_458
GTGACTGGCAATATAGGAAGATGCCGTGCTGCCTATACCTTTAATATCATAGCTATTGGATTCATCAGAGGGGAGAAGTT
ACCTGATGTTGTGATGAACCCACACCACTATTTCCTGACACAAATAACGAGCCAGTGCCCCTGAAAACAGGAGAAGATGA
CGATTACATGCTGGCCTTGAAACAGGAGTTAAGGGAAACAGTGACAGATTGCCTTAATTTATCGGAACACCCGAAAAAAA
TAAGATGATATTAAAGGTATAGCAAGTGATGCATGAAGGTCTATAAAGAAGAATGGGAACTAGATTGGAGAAGACTTCCA
AGAGAGATAATGCCAAGGAAAAAGTGAAAAAGAGCGGATCCAAAATCCAAACCGGCCAAAGCCACAAGCAAGGGTACTTT
CTCATGAATTCTGCAGATGTGTTGAAAAAGATTGAGGAACTGATAAGGAGAGGCGAGGGCGAAAGGTCGGATGAAGAAAA
CGATGGGAAAGAA

Alignment

ORF - retro_rnor_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 74.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAGNKGRGRAAYTFNIEAVGFSRGEKLPDVVL-KPPPLFPDTDYKPVPLKTGEDEDYMLALKQELRETVK
          ..GN.GR.RAAYTFNI.A.GF.RGEKLPDVV...P.PLFPDT...PVPLKTGED.DYMLALKQELRETV.
Retrocopy VTGNIGRCRAAYTFNIIAIGFIRGEKLPDVVM<EPTPLFPDTNNEPVPLKTGEDDDYMLALKQELRETVT

Parental  -RLPYFIETPEEKQ-DDIE-RYSKRYMKVYKEEWEPDWRRLPREMMPRKKCKKADPKSKAAKATSKGT-T
          .RLP.FI.TPE....DDI..RYSK..MKVYKEEWE.DWRRLPRE.MPRKK.K.ADPKSK.AKATSKGT..
Retrocopy <RLP*FIGTPEKNK<DDIK<RYSK*CMKVYKEEWELDWRRLPREIMPRKK*KRADPKSKPAKATSKGT<F

Parental  LMNSTDVLKKIEELERRGEGERSDEENDEKE
          LMNS.DVLKKIEEL.RRGEGERSDEEND.KE
Retrocopy LMNSADVLKKIEELIRRGEGERSDEENDGKE

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	5.25 RPM
SRP017611_kidney	0.00 RPM	18.21 RPM
SRP017611_liver	0.00 RPM	8.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_458 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006306	1 retrocopy	retro_chof_125,
Callithrix jacchus	ENSCJAG00000010747	1 retrocopy	retro_cjac_2691,
Echinops telfairi	ENSETEG00000008379	1 retrocopy	retro_etel_1040,
Homo sapiens	ENSG00000113356	2 retrocopies	retro_hsap_1454, retro_hsap_1885,
Gorilla gorilla	ENSGGOG00000000266	2 retrocopies	retro_ggor_1119, retro_ggor_1382,
Myotis lucifugus	ENSMLUG00000014954	1 retrocopy	retro_mluc_2233,
Macaca mulatta	ENSMMUG00000018972	1 retrocopy	retro_mmul_1332,
Nomascus leucogenys	ENSNLEG00000013749	1 retrocopy	retro_nleu_1807,
Otolemur garnettii	ENSOGAG00000005560	1 retrocopy	retro_ogar_3512,
Pongo abelii	ENSPPYG00000015624	1 retrocopy	retro_pabe_1564,
Pan troglodytes	ENSPTRG00000017068	2 retrocopies	retro_ptro_1266, retro_ptro_989,
Rattus norvegicus	ENSRNOG00000016260	2 retrocopies	retro_rnor_458 , retro_rnor_503,
Ictidomys tridecemlineatus	ENSSTOG00000008664	1 retrocopy	retro_itri_18,
Tupaia belangeri	ENSTBEG00000002278	2 retrocopies	retro_tbel_2495, retro_tbel_3069,