RetrogeneDB ID: retro_rnor_2629

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:58976842..58977284(-)
• Located in intron of: ENSRNOG00000006864

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2j2
• Ensembl ID: ENSRNOG00000019749
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 J2 [Source:RefSeq peptide;Acc:NP_001007656]

Sequence

>retro_rnor_2629
ATGAGCAGTAACAGCAGTAAGAGAGCAACAACAACAACAAAAGGGTGAAAGAGGACTACCTTCCAATTAAGAAAGACCCA
GTGCCTTACATCTGTGCGGAGCACCCCTCCCTTCAAATATTCTTGAATGGCATTATGTTGTCCAAGGTCCTGAGATGACT
CCTTATGAAGGTGGCTATTATCATGGAAAACTAATTTTTCTCAGAGAATTTCCATTTAAGCCTCCTAGTATTTACATGAT
AACCCCCAATGGAAGATTTAAGTGCAACACAAGGCTATGTCTCTCCATCACAGATTTCTACCCAGATACATGGAATACAG
CGCGGTCTGTCTCCACCATTCTAACAGGACTCCTGAGCTTTATGGTGGAGAAAGGCTCTACCCTAGGGAGCATAGAGACA
TTGGACTTCACGAAAAAATAGCTGGTAGTAAAGAGTCTAGTG

Alignment

ORF - retro_rnor_2629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.85 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSNSNKRAPTTATQRLKQDYLRIKKDP-VPYICAEPLPSNILEWHYVVRGPEMTPYEGGYYHGKLIFPR
          MSSNS.KRA.TT.T...K.......K.......C..PLPSNILEWHYVV.GPEMTPYEGGYYHGKLIF.R
Retrocopy MSSNSSKRA-TTTTKG*KRTTFQLRKTQ>ALHLCGAPLPSNILEWHYVVQGPEMTPYEGGYYHGKLIFLR

Parental  EFPFKPPSIYMITPNGRFKCNTRLCLSITDFHPDTWNPAWSVSTILTGLLSFMVEKGPTLGSIETSDFTK
          EFPFKPPSIYMITPNGRFKCNTRLCLSITDF.PDTWN.A.SVSTILTGLLSFMVEKG.TLGSIET.DFTK
Retrocopy EFPFKPPSIYMITPNGRFKCNTRLCLSITDFYPDTWNTARSVSTILTGLLSFMVEKGSTLGSIETLDFTK

Parental  KQLAAQSLV
          K.L...SLV
Retrocopy K*LVVKSLV

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	0.07 RPM	30.48 RPM
SRP017611_kidney	0.00 RPM	31.82 RPM
SRP017611_liver	0.00 RPM	19.43 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2629 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2629 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006403	1 retrocopy	retro_meug_1459,
Mus musculus	ENSMUSG00000023286	1 retrocopy	retro_mmus_1282,
Ochotona princeps	ENSOPRG00000002927	1 retrocopy	retro_opri_669,
Rattus norvegicus	ENSRNOG00000019749	1 retrocopy	retro_rnor_2629 ,