RetrogeneDB ID: retro_rnor_580

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:51736120..51736595(-)
• Located in intron of: ENSRNOG00000013975

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD620382
• Ensembl ID: ENSRNOG00000018397
• Aliases: Dnph1, C6orf108, RGD620382, Rcl
• Description: Deoxyribonucleoside 5'-monophosphate N-glycosidase [Source:UniProtKB/Swiss-Prot;Acc:O35820]

Sequence

>retro_rnor_580
GTGGTGGCATCAGGGGAGCAGGCTCCACGCTCCTTGTACTTCTGCAGGAGCATCTCGGCGGGCAAGTGGACCAAGTACTG
TATGTGCGGATCGTGTCGCGGGTGTGGCGCTATGGGAAGGTGCTCACTGAGCACGTGGATGACGCTGAGTTGGAGCCGCG
TGGGGAAGAGACTGCTGGGGGCGACCAGTTCATTCAAGAGCAGGACCTCAGCTGGCTGCAGCAAGCAGATGTGGTAGTGG
CCGAAGGGACACAGCCATCCTTGGGTGTTGGCTATGAATTGGGCGGGGCAGTAACTCTTGGAAGCCAATTCTATGCCTGT
TTCGACCACAGTCTGGCCGAGTGCTTTCCGCCATGATCCGCGGAGCAGCAGATGACTGGAGGTTCCAGGTATGGGACTAT
GCAGAGGGAGAAGTGCAGGCCATGATCGATCGGTACATTGAGGCATATCTTCCTCAGAAGACGGCTTCCTTTTCC

Alignment

ORF - retro_rnor_580 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 97.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASGEQAPCSVYFCGSIR-GGREDQALYARIVSRLRRYGKVLTEHVADAELEPLGEEAAGGDQFIHEQD
          ..ASGEQAP.S.YFC.SI..GG..DQ.LY.RIVSR..RYGKVLTEHV.DAELEP.GEE.AGGDQFI.EQD
Retrocopy VVASGEQAPRSLYFCRSIS<GGQVDQVLYVRIVSRVWRYGKVLTEHVDDAELEPRGEETAGGDQFIQEQD

Parental  LNWLQQADVVVAEVTQPSLGVGYELGRAVALG-KPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGE
          L.WLQQADVVVAE.TQPSLGVGYELG.AV.LG.KPILCLFRPQSGRVLSAMIRGAAD..RFQVWDYAEGE
Retrocopy LSWLQQADVVVAEGTQPSLGVGYELGGAVTLG<KPILCLFRPQSGRVLSAMIRGAADDWRFQVWDYAEGE

Parental  VETMLDRYFEAYLPQKTASSS
          V..M.DRY.EAYLPQKTAS.S
Retrocopy VQAMIDRYIEAYLPQKTASFS

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	2.66 RPM
SRP017611_kidney	0.14 RPM	1.74 RPM
SRP017611_liver	0.87 RPM	5.04 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_580 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_580 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_580 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012390	1 retrocopy	retro_amel_1012,
Bos taurus	ENSBTAG00000019913	1 retrocopy	retro_btau_518,
Canis familiaris	ENSCAFG00000001837	1 retrocopy	retro_cfam_1148,
Callithrix jacchus	ENSCJAG00000005337	1 retrocopy	retro_cjac_3948,
Equus caballus	ENSECAG00000006660	1 retrocopy	retro_ecab_595,
Felis catus	ENSFCAG00000009722	1 retrocopy	retro_fcat_365,
Homo sapiens	ENSG00000112667	1 retrocopy	retro_hsap_2562,
Nomascus leucogenys	ENSNLEG00000000516	1 retrocopy	retro_nleu_1515,
Pongo abelii	ENSPPYG00000016635	1 retrocopy	retro_pabe_1888,
Pan troglodytes	ENSPTRG00000029662	1 retrocopy	retro_ptro_1493,
Pteropus vampyrus	ENSPVAG00000008743	1 retrocopy	retro_pvam_1400,
Rattus norvegicus	ENSRNOG00000018397	1 retrocopy	retro_rnor_580 ,
Tursiops truncatus	ENSTTRG00000007022	1 retrocopy	retro_ttru_1520,