RetrogeneDB ID: retro_rnor_1602

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:9109805..9110266(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047161
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ube2l3
• Ensembl ID: ENSRNOG00000001862
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 L3 [Source:RefSeq peptide;Acc:NP_001102317]

Sequence

>retro_rnor_1602
ATGGCGGCCAGCAGGAGGGTGATGAAGGAGCTTGAAGAGATCTGCAAATGTGGAATGAAAAACTTCCATAACATCCAGGT
TGATGAAGCTAATTTATTGACTTGGCAAGGGCTTATTGTTCCTGACAACCCTCCCTATGATAAGGGAGCCTTCAGAATTG
AGATCTACTTCCCAGCAGAGTATTCCTTCAAGGCTCCCAAGATCACATTTAAAACAATGATCTACCATCCTAACATCGAC
AAGAAGGGGAGGTCTGTTTGCCCATAATTAGTGTGGAAAACTGGAAGCCAGCCATGAAGACTAACAAAGTAATCCAGTCT
CACATAGCACTGGTGAATGACCCCCAGCCTGAGCACCCACCCTGGGCTGACTTAGCTGAAGAATACTCTAAGGACTGTAA
AAAATTTTCTAAGAATGCTGAAGAGTTTACAAAGAAATATGGGGAAAAGCAACCTGTGGAT

Alignment

ORF - retro_rnor_1602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITF
          MAASRR.MKELEEI.KCGMKNF.NIQVDEANLLTWQGLIVPDNPPYDKGAFRIEI.FPAEY.FK.PKITF
Retrocopy MAASRRVMKELEEICKCGMKNFHNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEIYFPAEYSFKAPKITF

Parental  KTKIYHPNIDEK-GQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCKN
          KT.IYHPNID.K.G.VCLP.IS.ENWKPA.KT..VIQS.IALVNDPQPEHP..ADLAEEYSKD.KKF.KN
Retrocopy KTMIYHPNIDKK<GEVCLPIISVENWKPAMKTNKVIQSHIALVNDPQPEHPPWADLAEEYSKDCKKFSKN

Parental  AEEFTKKYGEKRPVD
          AEEFTKKYGEK.PVD
Retrocopy AEEFTKKYGEKQPVD

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	75.56 RPM
SRP017611_kidney	0.00 RPM	93.65 RPM
SRP017611_liver	0.00 RPM	42.70 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1602 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1602 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090,
Cavia porcellus	ENSCPOG00000006044	2 retrocopies	retro_cpor_692, retro_cpor_835,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Monodelphis domestica	ENSMODG00000017665	2 retrocopies	retro_mdom_2029, retro_mdom_956,
Mus musculus	ENSMUSG00000038965	10 retrocopies	retro_mmus_1619, retro_mmus_1620, retro_mmus_2147, retro_mmus_2212, retro_mmus_2272, retro_mmus_2315, retro_mmus_3205, retro_mmus_3714, retro_mmus_541, retro_mmus_995,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Rattus norvegicus	ENSRNOG00000001862	4 retrocopies	retro_rnor_1602 , retro_rnor_2633, retro_rnor_2799, retro_rnor_526,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Rattus norvegicus	ENSRNOG00000013741	9 retrocopies	retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539, retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,