RetrogeneDB ID: retro_rnor_1503

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:78972269..78973092(+)
• 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_1503
GAGTTCTCAGGGAAGCCAGCTGCTCGGAAAGCTCTGGACAGATGCAGTGAAGGCTCCTTCTTGCTAACCACGTTTCCTCG
GCCTGCGACTGTGGAGCCTATGGACCAGTTAGATGATGAAGAGGGACTCCCGGAGGAGCTGGTTCTAAAAAACCAGCAAT
TTCACGAGGAGAGAGAACAGCCACCCAGATTTGCACAGCCTGGGTCCTTTGAGAAGGAGTATACCATGCGCTGGAAGGCT
CTCATTGAGATAGAGAAGCAACAGCAGGATCAAGTGGATCGAAACATCGAGCAGGCTCGTGAGAAGATGGAGATGGAGGC
AGCACGCGTGAGCACCAGGTTATGCTAATGAGGCAGGATTTGATGAGACGTCAAGAAGAGCTTCGAAGAACGGAGGAGCT
GCATAACCAAGAGGTTCAGAAGCGATAGCGGTTAGAACTCAGGCAGGAAGAGGAACGCAGGCGCCGTGAGGAAGAGATGC
GGCGACAGCAGGAAGAAATGATGCGAGGGCAGCGGGAAGGACTCAAGGGAACCTTCCCTGATGCGAGAGAACAAGAGATA
CGGATGAGCAAATGGCTATGGGAGGTGCTGTGGACATAAACAGTAGAGGCGCCATGCCCCCTGCTCCTGTGCCACCAGGT
ACTCCAACTCCTGGACCTGCCATCATGATGCCAGATGGAACCCTGGGATTGACCCCAACAACAACTGAACGTTTTGGCCA
AGCTGCTACAATGGAAGGAATTGGAGCAATTGGTGGAACTCCTCCTGCATTCAACCGTCCAGCTCCTGGAGCTGAATTTG
CTCCAAATAAACGCCGCCGATAT

Alignment

ORF - retro_rnor_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSF
          EFSGKPAARKALDRCSEGSFLLTTFPRP.TVEPMDQLDDEEGLPE.LV.KNQQFH.EREQPPRFAQPGSF
Retrocopy EFSGKPAARKALDRCSEGSFLLTTFPRPATVEPMDQLDDEEGLPEELVLKNQQFHEEREQPPRFAQPGSF

Parental  EYEYAMRWKALIEMEKQQQDQVDRNIKEAREKLEMEMEAAR-HEHQVMLMRQDLMRRQEELRRMEELHNQ
          E.EY.MRWKALIE.EKQQQDQVDRNI..AREK..MEMEAAR..EHQVMLMRQDLMRRQEELRR.EELHNQ
Retrocopy EKEYTMRWKALIEIEKQQQDQVDRNIEQAREK--MEMEAAR<REHQVMLMRQDLMRRQEELRRTEELHNQ

Parental  EVQKRKQLELRQEEERRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMG-QMAMGGAMGINNRGAM
          EVQKR..LELRQEEERRRREEEMRRQQEEMMR.Q.EG.KGTFPDAREQEIRM..QMAMGGA..IN.RGAM
Retrocopy EVQKR*RLELRQEEERRRREEEMRRQQEEMMRGQREGLKGTFPDAREQEIRMS<QMAMGGAVDINSRGAM

Parental  PPAPVPPGTPAPPGPAAMMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRPAPGAEFAPNKRRRY
          PPAPVPPGTP..PGPA.MMPDGTLGLTP.TTERFGQAATMEGIGAIGGTPPAFNRPAPGAEFAPNKRRRY
Retrocopy PPAPVPPGTPT-PGPAIMMPDGTLGLTPTTTERFGQAATMEGIGAIGGTPPAFNRPAPGAEFAPNKRRRY

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_1503 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1503 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,