RetrogeneDB ID: retro_rnor_2188

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:166048916..166049356(+)
• Located in intron of: ENSRNOG00000043039

Retrocopy information

• Ensembl ID: ENSRNOG00000049752
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2h
• Ensembl ID: ENSRNOG00000048205
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2H [Source:RefSeq peptide;Acc:NP_001165598]

Sequence

>retro_rnor_2188
AAGTTTTATGGACCACAGGGAACTCCATATGAAGGTGGGGTGTGGAAAGTTAGAGTGGACCTTCGTGATAAATACCCTTT
CAAATCTCCATCTGTAGGATTCATGAATAAAATTTTCCTTCCTCACATTGATGAAGCGTCAGGAACTGTGTGTCTAGATG
TAATTAATCAAACTTGGACAGCTCTCTATGATCTTACCAATATATTTGAGGCCTTTGTGCCCCAGTTGCTGGCCTATCCT
AACCCCATAGATCCTCTCAATGGTGTCACTGCTGCAGCCATGTACCTCCACCGACCAGAGAAATACAAGCAGAAAATTAA
AGAGTACGTCCTGAAGTATGCAACGGAGGCCTGAAGGAACCGAAGAAGGGCACTGGTGACAGCTCATTGGAGAGTTCTAT
GTCTGACTAATCAGAAGCTGAGGCCCAGGACAAGGAGTTG

Alignment

ORF - retro_rnor_2188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 84.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDGSSRTVCLDVINQTWTALYDLTNIFE
          KFYGPQGTPYEGGVWKVRVDL.DKYPFKSPS.GFMNKIF.P.ID..S.TVCLDVINQTWTALYDLTNIFE
Retrocopy KFYGPQGTPYEGGVWKVRVDLRDKYPFKSPSVGFMNKIFLPHIDEASGTVCLDVINQTWTALYDLTNIFE

Parental  SFLPQLLAYPNPIDPLNG-DAAAMYLHRPEEYKQKIKEYIQKYATEEA-LKEQEEGTGDSSSESSMSDFS
          .F.PQLLAYPNPIDPLNG..AAAMYLHRPE.YKQKIKEY..KYAT.EA.LKE...GTGDSS.ESSMSD.S
Retrocopy AFVPQLLAYPNPIDPLNGVTAAAMYLHRPEKYKQKIKEYVLKYAT-EA<LKEPKKGTGDSSLESSMSD*S

Parental  EDEAQDMEL
          E.EAQD.EL
Retrocopy EAEAQDKEL

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	143.15 RPM
SRP017611_kidney	0.00 RPM	96.79 RPM
SRP017611_liver	0.00 RPM	109.19 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2188 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003605	2 retrocopies	retro_chof_1862, retro_chof_1932,
Callithrix jacchus	ENSCJAG00000010520	1 retrocopy	retro_cjac_1081,
Homo sapiens	ENSG00000186591	1 retrocopy	retro_hsap_3977,
Nomascus leucogenys	ENSNLEG00000012685	1 retrocopy	retro_nleu_2037,
Pongo abelii	ENSPPYG00000017997	1 retrocopy	retro_pabe_3271,
Rattus norvegicus	ENSRNOG00000048205	2 retrocopies	retro_rnor_2188 , retro_rnor_2266,