RetrogeneDB ID: retro_rnor_1178

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:12640718..12641737(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nono
• Ensembl ID: ENSRNOG00000003689
• Aliases: None
• Description: Non-POU domain-containing octamer-binding protein [Source:UniProtKB/Swiss-Prot;Acc:Q5FVM4]

Sequence

>retro_rnor_1178
CACCATCAACATCACCACCACCACCAGAAGCAGCAGGAGCAGCAGCAGCAGCAGCCACCTCCACGAATACCTGCAAATGG
ACAGCATTCCAGCAGCCAGAATGAAGGCTTGACTATTGACTTGAAGAATTTTAGGAGTGAGAAGACCTTTACCAATATAG
CCATCTCTTTGTGGGCAATCTTCCTCCTGACATTACTGAGGAAGAAATGAGGAAGCTTTTTGAGAAATATGGAAAAGCAG
AAGTTTTCACTCATGAGGAAAAAGGCTTTTACTTTATTCTCTTGGAATCAGGAACCCTAATGGAAATTGCCAAAGTGGAG
CTGGACAATACTCCACTCTGTGCAAAGCAACTGCAAGCGCTCTTTCCTTGTCATAGTGCAATCCTTACAGCCCACAGCCT
TCCTCAGATTGTGTCCAGTGAACTGCTGAAAGAACCTTTCTCTGGGTTTGGCCAGGTGGAGAGGGCTGTATTCATTGTAA
ATGACTGAAGAAGGCCCTGAGAGAAAGGCATTTTGAGTTCTCATTGAAGCCAGCTACTCAGAAAGCTCTGAGCAGATGCA
GTGAAGGCTCATTCTTGCTAACCACATTTCCTCAGCCTGTCACTGTAGAGCCTATGGACTGGTTAGATAATGAAGAGAGA
CTTCCAGAGAAGCTGATTATAAATAAGACGCAATTTCACAAGGAGAGAGAACAGTCACCCAGATTCGCACAGCCTGGGTC
CTGTGAGTATGAGTATGGTGTGCACTGGAAGGCACTCACTGAGATGGAGAAGCAACAGCAGGAGCAAGTGGACCGGAAGA
TCAAGGAGGCTTGTGCGAGGCTGGAGATGGAGATGGAGGCAACACAGCATGGGCACCAGGTTACGCTAATGAGGAAGGAG
TTGATGAGACATCAATAAGAGCTTTGAAAAATGGAGGAGCTGCATAACCAAGAGGTTCAGAAATGAAAGCAGTTAGAACT
GAGGCAGGTAGAGGAATGAGATGCAGAAACAGGAAGAAATGATGTGACAGGAGCAGGAA

Alignment

ORF - retro_rnor_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.52 %
• Parental protein coverage: 72.06 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HQQHHQQQQQQQQQQQQQPPPPIPANGQQASSQNEGLTIDLKNFRKPGEKTFT-QRSRLFVGNLPPDITE
          H.QHH..............PP.IPANGQ..SSQNEGLTIDLKNFR...EKTFT.Q.S.LFVGNLPPDITE
Retrocopy HHQHHHHHXXXXXXXXXXXPPRIPANGQHSSSQNEGLTIDLKNFRS--EKTFT<QYSHLFVGNLPPDITE

Parental  EEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQ
          EEMRKLFEKYGKA.EVF.H..KGF.FI.LE..TL.EIAKVELDN.PL..KQL...F.CHSA.LT...LPQ
Retrocopy EEMRKLFEKYGKA-EVFTHEEKGFYFILLESGTLMEIAKVELDNTPLCAKQLQALFPCHSAILTAHSLPQ

Parental  YVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIV-EFSGKPAARKALDRCSEGSFLLTTFPRPVTVEP
          .VS.ELL.E.FS.FGQVERAV.IV.D..RP..KGI..EFS.KPA..KAL.RCSEGSFLLTTFP.PVTVEP
Retrocopy IVSSELLKEPFSGFGQVERAVFIVND*RRP*EKGIL<EFSLKPATQKALSRCSEGSFLLTTFPQPVTVEP

Parental  MDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDRNIKEAREKL
          MD.LD.EE.LPEKL.I...QFHKEREQ.PRFAQPGS.EYEY...WKAL.EMEKQQQ.QVDR.IKEA...L
Retrocopy MDWLDNEERLPEKLIINKTQFHKEREQSPRFAQPGSCEYEYGVHWKALTEMEKQQQEQVDRKIKEACARL

Parental  EMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEE-RRRREEEMRRQQEE
          EMEMEA..H.HQV.LMR..LMR.Q.EL..MEELHNQEVQK.KQLELRQ.EE......EEM..Q..E
Retrocopy EMEMEATQHGHQVTLMRKELMRHQ*EL*KMEELHNQEVQK*KQLELRQVEE>EMQKQEEMM*QEQE

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	105.11 RPM
SRP017611_kidney	0.00 RPM	128.05 RPM
SRP017611_liver	0.00 RPM	55.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1178 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438, retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178 , retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,