RetrogeneDB ID: retro_rnor_868

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:21231180..21231735(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccdc90b
• Ensembl ID: ENSRNOG00000009462
• Aliases: Ccdc90b, RGD1308637
• Description: Coiled-coil domain-containing protein 90B, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q4V897]

Sequence

>retro_rnor_868
ATTTCAACTCCCCACGGGTGTCTGTCACCCGCCCTGCGGAGAGTTTTCTTGACCACCACAACTAAGTCGGGTTATGATAG
AAAACCAGTGGGCATAACTCCTCTAGAATAAAGAAAATTAACTTTTGATACCCATGCGTGGGTGCAGGAGGGGGAAACTC
ACGGATTTGACAAAACACAAGCACAGGCGATTGTATCGGTACTAAGTACGTTATCAAATGTCTCCTTGGATACGATCTAC
AAGGAAATGGTGAGTAAAGCTCAACAGGAAATAACCGTGCAGCAGCTAATGGCTCATTTGGATTCCGTAAGAAAAGACAT
GGTCATCCTAGAGAAAATTGAATTTGCAAATCCGAGAGCAGAGAATGAGAAAATGAAAACTGAACTAGATCAAGTGAAGC
AGCAGTTGACTAATGAAACCACTCGAGTCAGAGCGGACAATCAGCTGGACATCAACCTGGAACGGAGCAGAGCGACAGAC
ATGTTCACAGATTAAGAAAAGCAACTTATGGAAGCAACCAATGAGTTTACCAAAAAGGATACACAAACCAGTAAT

Alignment

ORF - retro_rnor_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 72.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISSPHGRLSPALRRGFLTTTTKSDYDRRPVEITPLEQRKLTFDTHALVQDLETHGFDKGQAQTIVSVLST
          IS.PHG.LSPALRR.FLTTTTKS.YDR.PV.ITPLE.RKLTFDTHA.VQ..ETHGFDK.QAQ.IVSVLST
Retrocopy ISTPHGCLSPALRRVFLTTTTKSGYDRKPVGITPLE*RKLTFDTHAWVQEGETHGFDKTQAQAIVSVLST

Parental  LSNVSLDTVYKEMVTKAQQEITIQQLMAHLDSIRKDMVILEKSEFANLRAENEKMKIELDQVKQQLINET
          LSNVSLDT.YKEMV.KAQQEIT.QQLMAHLDS.RKDMVILEK.EFAN.RAENEKMK.ELDQVKQQL.NET
Retrocopy LSNVSLDTIYKEMVSKAQQEITVQQLMAHLDSVRKDMVILEKIEFANPRAENEKMKTELDQVKQQLTNET

Parental  SRIRADNRLDINLERSRVTDMFTDQEKQLMEATNEFTKKDMQTKS
          .R.RADN.LDINLERSR.TDMFTD.EKQLMEATNEFTKKD.QT..
Retrocopy TRVRADNQLDINLERSRATDMFTD*EKQLMEATNEFTKKDTQTSN

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	0.29 RPM	7.84 RPM
SRP017611_kidney	1.05 RPM	11.51 RPM
SRP017611_liver	0.81 RPM	4.64 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_868 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_868 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880, retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868 ,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366,