RetrogeneDB ID: retro_rnor_2918

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:46103994..46104687(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnf41
• Ensembl ID: ENSRNOG00000023456
• Aliases: None
• Description: E3 ubiquitin-protein ligase NRDP1 [Source:RefSeq peptide;Acc:NP_001012195]

Sequence

>retro_rnor_2918
CAGCAGACATATTCCATAGACCATAGCATTGTCACGGTTGCCCACCTGTGCCCAGTACCTCTGATCGTGCGGACCATGTT
GTCAAACTATAGATTGCCTGTGACAACTCTGTGTTTGGCTGCAGTGCTCTTGTTAGACTTGACAACCTCATGCCCCACCT
CAGTGACTGTGAGTACAACCCAAAGCAGCTGTGACCGGTGAGCAAGGCTGTGGCCTGGAGATGCCCAAAGATGAACGGCC
AAACTATAATTGCATTAAGAACCTGTGCTCCAAGGTCAAGCAGCAGGAGACGTGCATTGCAGAGCAGGAGAAGACATCTG
CTGAACACAAGCACCAGCTGGCAGAAGAGAAAGGAAACATTCACTCCTGAAGGGATATATGCAAACAATCCACAGAGTCA
ACCCCAACCTTCAGAACCTGGAAGAGACAATCGAGTACAACAAGATCCTCAAGAGGGTGAACCCCCTACAGCCGGCAAGA
GTGACCCACTAGGGAGGGCTGATCTCCACTCCTGACTCTGTGCTCCAGGCTGTAATCAAGTGTTTCTCTGTGGAAAGTGA
CTGCCACCCAGCCTCTACAGTCAATGAGCTGGTGACAAAGCCCAGTGAATGTAGCTGGCCCCAGGGTCTGACTGCACTAG
AGACAAGACAGATGAGAACCATGTGGCCAAGTGCATCCCTGGCAAGCAGGCTA

Alignment

ORF - retro_rnor_2918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.36 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QQTCPVDRSVVTVAHLRPVPRIMRNMLS-KLQIACDNAVFGCSAVVRLDSLMSHLSDCEHNPKR-PVTCE
          QQT...D.S.VTVAHL.PVP.I.R.MLS.KL.IACDN.VFGCSA.VRLD.LM.HLSDCE.NPK...VT.E
Retrocopy QQTYSIDHSIVTVAHLCPVPLIVRTMLS<KL*IACDNSVFGCSALVRLDNLMPHLSDCEYNPKQ<AVTGE

Parental  QGCGLEMPKDELPNHNCIKHLRSVVQQQQTRIAELEKTSAEHKHQLAEQKRDIQ-LLKAYMRAIRSVNPN
          QGCGLEMPKDE.PN.NCIK.L.S.V.QQ.T.IAE.EKTSAEHKHQLAE.K..I..LLK.YM..I..VNPN
Retrocopy QGCGLEMPKDERPNYNCIKNLCSKVKQQETCIAEQEKTSAEHKHQLAEEKGNIH<LLKGYMQTIHRVNPN

Parental  LQNLEETIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGC-PASIVNELIENAHERSW
          LQNLEETIEYN.IL..VN.LQPARVT..GG.ISTPD.VLQAVIK...VES.C.PAS.VNEL.....E.SW
Retrocopy LQNLEETIEYNKILKRVNPLQPARVTH*GGLISTPDSVLQAVIKCFSVESDCHPASTVNELVTKPSECSW

Parental  PQGLATLETRQMNRRYYENYVAKRI
          PQGL..LETRQM.........A.R.
Retrocopy PQGLTALETRQMRTMWPSASLASRL

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	44.50 RPM
SRP017611_kidney	0.00 RPM	20.03 RPM
SRP017611_liver	0.00 RPM	9.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2918 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2918 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2918 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001320	1 retrocopy	retro_meug_901,
Meleagris gallopavo	ENSMGAG00000006916	1 retrocopy	retro_mgal_15,
Myotis lucifugus	ENSMLUG00000006057	1 retrocopy	retro_mluc_300,
Otolemur garnettii	ENSOGAG00000001525	4 retrocopies	retro_ogar_2365, retro_ogar_2487, retro_ogar_3113, retro_ogar_3228,
Rattus norvegicus	ENSRNOG00000023456	1 retrocopy	retro_rnor_2918 ,
Sarcophilus harrisii	ENSSHAG00000002679	1 retrocopy	retro_shar_38,