RetrogeneDB ID: retro_rnor_2550

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:13188396..13188831(+)
• Located in intron of: ENSRNOG00000009043

Retrocopy information

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

Parental gene information

• Parental gene symbol: Scnm1
• Ensembl ID: ENSRNOG00000021092
• Aliases: None
• Description: sodium channel modifier 1 [Source:RefSeq peptide;Acc:NP_001101166]

Sequence

>retro_rnor_2550
CCCCACCGACCAGCACTGGACCCGCTGGCCATGCTGATAGCCCTCCGTGCAGGCAAGAAGCACCTGTCCAGTCTGAAGCC
TTTCTATGGCAAAAGTCAGTCAGGCCAGGGAACAGAGCACAATCCAAGACAGTAGAATAAACTGAAGACAGAAAGCAAAG
CTGAGGCTCGAATAATTACCCAGAATGCTCTTCACAGAGCTCCCCACTATAACAGTTGCTGCTTGAGGAAGCACAGACCA
GAAGCCCCTGCTCCCTCTGTCCCCAGCTCTCTCTCCTTTGCTACCTCCAGAGGTCGAACTCCAGGGTGCAAAGATCAGTA
GGGAAGCTGAGCCCAGGGAGAGATCAGATGCCAAAGGGTCAGCAGCTCTCCTGGCCTCTGCACCCACGAGCCTCACAAAA
TGGCGAGCCCTGAACCATTCATCACCTTGCCCTCT

Alignment

ORF - retro_rnor_2550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 65.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PHRPVLDTLAMLTAHRAGKKHLSSLKLFYGKKQSGKGTEQNPRPQNELKTESKTEAPLLTQTRIITQNAL
          PHRP.LD.LAML.A.RAGKKHLSSLK.FYGK.QSG.GTE.NPR..N.L....KTE.......RIITQNAL
Retrocopy PHRPALDPLAMLIALRAGKKHLSSLKPFYGKSQSGQGTEHNPRQ*NKL----KTESK--AEARIITQNAL

Parental  HRAPHYNSCCRRKHRPEAPAPSVSSS-SVPTPEAELQSAK-ISKEPEPRQRSDAKKSPALSTSAPMSPTK
          HRAPHYNSCC.RKHRPEAPAPSV.SS.S..T........K.IS.E.EPR.RSDAK.S.AL..SAP.S.TK
Retrocopy HRAPHYNSCCLRKHRPEAPAPSVPSSLSFATSRGRTPGCK>ISREAEPRERSDAKGSAALLASAPTSLTK

Parental  RRVLNH-YLTLRS
          .R.LNH...TL.S
Retrocopy WRALNH<FITLPS

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	6.18 RPM
SRP017611_kidney	0.00 RPM	15.07 RPM
SRP017611_liver	0.00 RPM	3.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2550 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2550 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004323	1 retrocopy	retro_dnov_1019,
Oryctolagus cuniculus	ENSOCUG00000026766	1 retrocopy	retro_ocun_925,
Rattus norvegicus	ENSRNOG00000021092	1 retrocopy	retro_rnor_2550 ,