RetrogeneDB ID: retro_rnor_912

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:39931735..39932077(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2s
• Ensembl ID: ENSRNOG00000016930
• Aliases: Ube2s, RGD1564746
• Description: Ubiquitin-conjugating enzyme E2 S [Source:UniProtKB/Swiss-Prot;Acc:B5DFI8]

Sequence

>retro_rnor_912
GACCCACTTGATGAAATTAAAGTCTTCCCCAGTGAGGAGGATGTCACTAACCTGCAGGTCAGTATGGAAGGCCTCAAGGG
GATCCCTTATGATGATAGCCTGTTTTGTGTGAAGTTCTTAGACAAGGATTTTCTGCCTCACCACCCAAGAGCTACTTCCT
GACCAAGATCTTCTAACCATATGTGGCTGTCAGTGGTGAAATCTGTGCCAACATGTTCAAGAGAGACTGACAACTGAGCA
GGGCATTGAACATGTGCTGCTGACCAAGTGCCTGGCAATGCATCTAACCCCTGGTCTGCATTGGACCAGGAGACAGGCTG
CCTGCTTTTGGAGAACTATGAG

Alignment

ORF - retro_rnor_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 52.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDF-PASPPKGYFLTKIFHPNVGPNGEI
          DP.D.IKVFP.EED.T.LQV..EG..G.PY...LF..K.L..KDF..ASPPK.YFLTKIF.P.V...GEI
Retrocopy DPLDEIKVFPSEEDVTNLQVSMEGLKGIPYDDSLFCVKFL-DKDF<SASPPKSYFLTKIF*PYVAVSGEI

Parental  CVNVLKRD-WTAELGIRHVLLTIKCLLIH-PNPESALNEEAGRLLLENYE
          C.N..KRD..T.E.GI.HVLLT.KCL..H..NP.SAL..E.G.LLLENYE
Retrocopy CANMFKRD<LTTEQGIEHVLLT-KCLAMH<SNPWSALDQETGCLLLENYE

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	32.28 RPM
SRP017611_kidney	0.00 RPM	13.96 RPM
SRP017611_liver	0.00 RPM	6.52 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_912 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_912 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_912 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000874	3 retrocopies	retro_cjac_1995, retro_cjac_3689, retro_cjac_406,
Homo sapiens	ENSG00000108106	1 retrocopy	retro_hsap_1808,
Mus musculus	ENSMUSG00000060860	2 retrocopies	retro_mmus_1675, retro_mmus_3278,
Pan troglodytes	ENSPTRG00000011507	2 retrocopies	retro_ptro_3055, retro_ptro_3059,
Rattus norvegicus	ENSRNOG00000016930	2 retrocopies	retro_rnor_1730, retro_rnor_912 ,