RetrogeneDB ID: retro_rnor_95

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:71248762..71248972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000049442
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rps28
• Ensembl ID: ENSRNOG00000042886
• Aliases: None
• Description: 40S ribosomal protein S28 [Source:UniProtKB/Swiss-Prot;Acc:P62859]

Sequence

>retro_rnor_95
ATGGACACGAGTCGCGTGCAGCCCATCAAGCTGGCTAGGGTAACTAAAGTGCTGGGCAGGACCGGATCGCAGGGACAGTG
CACGCAGGTGCGAGTGGAATTTATGGATGACACCAGCCGCTCTATCATCCGAAACGTCAAAGGCCCTGTTCGAGAGGGTG
ATGTGCTCACCCTGTTGGAGTCAGAAAGAGAAGCTCGGAGGTTGCGCTGA

Alignment

ORF - retro_rnor_95 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
          MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
Retrocopy MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR

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	0.14 RPM	18.33 RPM
SRP017611_kidney	0.56 RPM	37.61 RPM
SRP017611_liver	0.27 RPM	25.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_95 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_95 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_95 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Bos taurus	ENSBTAG00000002468	1 retrocopy	retro_btau_1130,
Cavia porcellus	ENSCPOG00000022876	5 retrocopies	retro_cpor_1092, retro_cpor_1485, retro_cpor_1504, retro_cpor_176, retro_cpor_702,
Equus caballus	ENSECAG00000017256	1 retrocopy	retro_ecab_725,
Felis catus	ENSFCAG00000024931	3 retrocopies	retro_fcat_1130, retro_fcat_611, retro_fcat_752,
Homo sapiens	ENSG00000233927	9 retrocopies	retro_hsap_1192, retro_hsap_1352, retro_hsap_1725, retro_hsap_2220, retro_hsap_2279, retro_hsap_3748, retro_hsap_505, retro_hsap_523, retro_hsap_799,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Myotis lucifugus	ENSMLUG00000023621	1 retrocopy	retro_mluc_2040,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Oryctolagus cuniculus	ENSOCUG00000021484	2 retrocopies	retro_ocun_1230, retro_ocun_1799,
Pan troglodytes	ENSPTRG00000040141	6 retrocopies	retro_ptro_1228, retro_ptro_1613, retro_ptro_3037, retro_ptro_378, retro_ptro_391, retro_ptro_927,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95 , retro_rnor_96,
Sus scrofa	ENSSSCG00000013597	3 retrocopies	retro_sscr_132, retro_sscr_191, retro_sscr_808,