RetrogeneDB ID: retro_rnor_1852

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:176373882..176374168(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004455
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bud31
• Ensembl ID: ENSRNOG00000000989
• Aliases: Bud31, Edg2, G10
• Description: None

Sequence

>retro_rnor_1852
ATGCCCAGAGTCAAAAGAAGCCAGAAAGCACCTCCAGCTAGCTGGGAGATGATCGAACCAATGTTGGATGAACTGGATCA
AAAGAGGAGAGAAGCTGAAACTGAACCCCGGGAGGGAAAAAGGAAAAGTGGAATCTCGGTGGCCCATCTTCAGAATCCAT
CACCAGAAAGCCCACTATGTCTTCGACCTCCTTTACAAGAGGAAAGCCATAAGCAGAGAAGTCTATGAATACTGCATGAA
GGAAGGCTATACAGACGAAAACCTGATTGCAAAGTGGAAGAAGCAG

Alignment

ORF - retro_rnor_1852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 65.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKVKRSRKAPPDGWELIEPTLDELDQKMREAETEPHEGKRK-VESLWPIFRIHHQKTRYIFDLFYKRKA
          MP.VKRS.KAPP..WE.IEP.LDELDQK.REAETEP.EGKRK.VES.WPIFRIHHQK..Y.FDL.YKRKA
Retrocopy MPRVKRSQKAPPASWEMIEPMLDELDQKRREAETEPREGKRK>VESRWPIFRIHHQKAHYVFDLLYKRKA

Parental  ISRELYEYCIKEGYADKNLIAKWKKQ
          ISRE.YEYC.KEGY.D.NLIAKWKKQ
Retrocopy ISREVYEYCMKEGYTDENLIAKWKKQ

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	23.51 RPM
SRP017611_kidney	0.00 RPM	19.89 RPM
SRP017611_liver	0.00 RPM	10.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1852 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1852 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006269	2 retrocopies	retro_amel_1325, retro_amel_997,
Bos taurus	ENSBTAG00000020439	1 retrocopy	retro_btau_1066,
Choloepus hoffmanni	ENSCHOG00000004055	1 retrocopy	retro_chof_1013,
Dipodomys ordii	ENSDORG00000000739	1 retrocopy	retro_dord_58,
Equus caballus	ENSECAG00000024151	2 retrocopies	retro_ecab_254, retro_ecab_672,
Ficedula albicollis	ENSFALG00000013804	1 retrocopy	retro_falb_27,
Homo sapiens	ENSG00000106245	1 retrocopy	retro_hsap_4712,
Gorilla gorilla	ENSGGOG00000015119	1 retrocopy	retro_ggor_2928,
Loxodonta africana	ENSLAFG00000012201	1 retrocopy	retro_lafr_24,
Macropus eugenii	ENSMEUG00000006920	1 retrocopy	retro_meug_446,
Microcebus murinus	ENSMICG00000017426	2 retrocopies	retro_mmur_470, retro_mmur_622,
Nomascus leucogenys	ENSNLEG00000011020	1 retrocopy	retro_nleu_2053,
Pongo abelii	ENSPPYG00000017376	2 retrocopies	retro_pabe_3313, retro_pabe_3660,
Pan troglodytes	ENSPTRG00000019451	1 retrocopy	retro_ptro_2735,
Pteropus vampyrus	ENSPVAG00000007527	1 retrocopy	retro_pvam_474,
Rattus norvegicus	ENSRNOG00000000989	1 retrocopy	retro_rnor_1852 ,
Tupaia belangeri	ENSTBEG00000010640	2 retrocopies	retro_tbel_2683, retro_tbel_4119,
Tursiops truncatus	ENSTTRG00000003005	1 retrocopy	retro_ttru_815,