RetrogeneDB ID: retro_rnor_2606

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:4562250..4562829(-)
• Located in intron of: ENSRNOG00000029148

Retrocopy information

• Ensembl ID: ENSRNOG00000022081
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ddi2
• Ensembl ID: ENSRNOG00000012274
• Aliases: Ddi2, RGD1311815
• Description: protein DDI1 homolog 2 [Source:RefSeq peptide;Acc:NP_001029321]

Sequence

>retro_rnor_2606
CAACATCAACGTATACCATCAACACAGCAAGCCCACGGATTGGCTTCTGGAGAGAATATGGCTTTTGCTCAGGATCTCAA
CAGCCCTGCCCTGATTCGAAGCATGCTGCTTTCCAACCCCCATGACCTGTCCCCTGTTGAAGGAACGGAATCCTGCTTTG
GCGGAAGCTCTGCTTAGTGGAAACCTCGAGACATTTCTTCAGGTCCTGGTGGAACAGCAGAGAGAAAGGGCCATGAGAGA
GCAAGAGATGTTTCGTCTTTATTCTGCTGACCCATTTGATCAGGAGACACAGGCTAGAATAGAAGAAGAAATCCGACAGC
AGAATATTGAAGAAAATATGAATATAGCCATGGAAGAGGCTCCGGAGAGTTTTGGACAAGTGGCTATGCTCTATATTAAC
TGCAAAGTGAACGGGCATCCTTTAAAGGCTTTTGTTGACTCAGGTGCCCAGATGACTATCATGAGCCAAGCTTGTGCTGA
GAGATGTAATATCATGAGACTGGTAGACCGACGGTGGGCTGGGGTTGCTAAGGGAGTAGGCACACAGAGGATTATGGGCC
GCGTTCATCTGGCTCAGAT

Alignment

ORF - retro_rnor_2606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.44 %
• Parental protein coverage: 64.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQRQLPRTQ-AQLLSPGERTSTPQGLDSPALLRDMLLANPHELS-LLKERNPPLAEALLSGDLEKFSRVL
          Q....P.TQ.A..L..GE.....Q.L.SPAL.R.MLL.NPH.LS.LLKERNP.LAEALLSG.LE.F..VL
Retrocopy QHQRIPSTQQAHGLASGENMAFAQDLNSPALIRSMLLSNPHDLS>LLKERNPALAEALLSGNLETFLQVL

Parental  VEQQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVAMLYINCRVNGH
          VEQQ..RA.REQE..RL.SADPFD.E.QA.IEE.IRQQNIEENM.IAMEEAPESFGQVAMLYINC.VNGH
Retrocopy VEQQRERAMREQEMFRLYSADPFDQETQARIEEEIRQQNIEENMNIAMEEAPESFGQVAMLYINCKVNGH

Parental  PVKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHL-GSD
          P.KAFVDSGAQMTIMSQACAERCNIMRLVDRRWAG.AKGVGTQ.I.GRVHL.GSD
Retrocopy PLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGTQRIMGRVHL<GSD

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	32.35 RPM
SRP017611_kidney	0.00 RPM	73.69 RPM
SRP017611_liver	0.00 RPM	124.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2606 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2606 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15, retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606 ,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,