RetrogeneDB ID: retro_rnor_473

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:115180856..115181458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000021484
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rhoq
• Ensembl ID: ENSRNOG00000015415
• Aliases: Rhoq, Tc10
• Description: Rho-related GTP-binding protein RhoQ [Source:UniProtKB/Swiss-Prot;Acc:Q9JJL4]

Sequence

>retro_rnor_473
ATGGCTCACGGCCCGGCGCGCTGATGCTCAAGTGCGTGGTGGTCGGCGACGGGGCGGTGGGTAAGAGGTGCCTGCTCATG
AGCTATGCCAACGACGCCTTCCCCGAGGAGTACGTGCCCACTGTCTTCGACAGCGTCACCGTGGGGGACAAGCAGTACCT
CTTGGGACTCTATGACACAGCTGGACAGGAAGACTATGATCGTCTGAGGCCTTTATCTTACCCCATGACTGACGTCTTCC
TCATATGCTTCTCTGTGGTAAATCCAGCCTCATTTCAAAATGTAAAGGAGGAATGGGTACCAGAACTAAAGGAATATGCA
CCAAATGTCCCCTTCTTGTTAATAGGAACTCAGATTGATCTCCGAGATGACCCCAAAACTTTAGCAAGACTGAATGACAT
GAAAGAAAAACCTGTCTGTGTGGAACAAGGACAGAAACTAGCAAAAGAGATCGGCGCATGCTGCTATGTGGAATGCTCAG
CTCTGACCCAGAAGGGTTTGAAGACTGTGTTTGACGAGGCTATCATAGCCATTTTAACTCCAAAGAAACACACAGTAAAA
AAGAGAATAGGATCAAGATGTATAAACTGTTGTTTGATTACG

Alignment

ORF - retro_rnor_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAHGP-GALMLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQED
          MAHGP.GALMLKCVVVGDGAVGK.CLLMSYANDAFPEEYVPTVFD....SVTVG.KQYLLGLYDTAGQED
Retrocopy MAHGP<GALMLKCVVVGDGAVGKRCLLMSYANDAFPEEYVPTVFD----SVTVGDKQYLLGLYDTAGQED

Parental  YDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLNDMK
          YDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLNDMK
Retrocopy YDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLNDMK

Parental  EKPVCVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTVKKRIGSRCINCCLIT
          EKPVCVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTVKKRIGSRCINCCLIT
Retrocopy EKPVCVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTVKKRIGSRCINCCLIT

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	0.07 RPM	17.33 RPM
SRP017611_kidney	0.00 RPM	25.54 RPM
SRP017611_liver	0.00 RPM	9.08 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_473 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_473 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383,
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468, retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000015608	1 retrocopy	retro_fcat_795,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Myotis lucifugus	ENSMLUG00000001567	1 retrocopy	retro_mluc_595,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Rattus norvegicus	ENSRNOG00000013536	1 retrocopy	retro_rnor_2062,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473 ,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,
Tursiops truncatus	ENSTTRG00000011892	1 retrocopy	retro_ttru_805,