RetrogeneDB ID: retro_rnor_550

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:268916534..268916903(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Josd2
• Ensembl ID: ENSRNOG00000019442
• Aliases: Josd2, RGD1307305
• Description: Josephin-2 [Source:RefSeq peptide;Acc:NP_001099726]

Sequence

>retro_rnor_550
ATGTCTCAGGCGGTGGAAGCGAGGTCAAGTCCACCCTCAGTGTATCAAGAGCGGCAGAGGCTAGAGCTGTGTGCCGTCCA
TGCTCTCAACAACGTCCTCCAAGAGCAGCTCTTTAGCCAGGAAGATGCTGACGAAATCTGCGAGAGGCTAGCCCCAGATT
CCCAACTGAACTCCCATCGCAGCCTCTTGGGCACTGGCAACTATGATATCAACGTGATCATGGCTGCTCTGTAGGGCCTG
GGCCTGGCTGCTGTGTGGTGGGAGAGGAGGAGACCCTTGTCCCAGTTAGTCCTGCTCCAGATAGTAGGCCTGATCTTGAA
CCTACCCTCTCCTGTGTCACCGGGGCTGTGCCAGGTGGCCCTGCGCCAG

Alignment

ORF - retro_rnor_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.93 %
• Parental protein coverage: 65.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQAPEARPRSPSVYHERQRLELCAVHALNNVLQEQLFSQEAADEICKRLAPDSRLNPHRSLLGTGNYDV
          MSQA.EAR...PSVY.ERQRLELCAVHALNNVLQEQLFSQE.ADEIC.RLAPDS.LN.HRSLLGTGNYD.
Retrocopy MSQAVEARSSPPSVYQERQRLELCAVHALNNVLQEQLFSQEDADEICERLAPDSQLNSHRSLLGTGNYDI

Parental  NVIMAALQGLGLAAVWWDRRRPLSQLVLPQVLGLILNLPSPVSLGLLSLPLRR
          NVIMAAL.GLGLAAVWW.RRRPLSQLVL.Q..GLILNLPSPVS.GL....LR.
Retrocopy NVIMAAL*GLGLAAVWWERRRPLSQLVLLQIVGLILNLPSPVSPGLCQVALRQ

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	20.63 RPM
SRP017611_kidney	0.00 RPM	10.40 RPM
SRP017611_liver	0.00 RPM	10.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_550 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_550 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_550 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000014440	2 retrocopies	retro_rnor_2954, retro_rnor_906,
Rattus norvegicus	ENSRNOG00000019442	1 retrocopy	retro_rnor_550 ,