RetrogeneDB ID: retro_rnor_1118

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:72538540..72538833(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP9
• Ensembl ID: ENSRNOG00000007972
• Aliases: None
• Description: Putative hydrolase RBBP9 [Source:UniProtKB/Swiss-Prot;Acc:O88350]

Sequence

>retro_rnor_1118
CTGCTGTTCATGCAGGCAGAGCTGTACTGTGATGAGAATACAATCTTTGTAGACCACAGTTCTGGGACAATGGTGGTCAT
GATGTATACCAAAACCCATTAAGTATATGCAATTGTATTGATGTCTGCATGTATATCAGACTTCAAGGATGAAAGTGAGC
ATTTAAGTTGGTACTTTAGTCACCCCCAGCCCCAACAATGGGAAAAGATCAAACCCTACCTCCCTCACATTATACAGTTT
GGCTTTGCTGATGACCCCTTCCCTCATGGAAGGAACAACAAGAAGTGGCAGAC

Alignment

ORF - retro_rnor_1118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.61 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPFMETELHCDEKTIIIGHSSGAIAAMRYAETHQVYALILVSAYTSDLGDENERASGYFS--RPWQWEKI
          L.FM..EL.CDE.TI...HSSG....M.Y..TH.VYA..L.SA..SD..DE.E..S.YFS...P.QWEKI
Retrocopy LLFMQAELYCDENTIFVDHSSGTMVVMMYTKTH*VYAIVLMSACISDFKDESEHLSWYFSHPQPQQWEKI

Parental  KANCPHIIQFGSTDDPF-LPWKEQQEVAD
          K...PHIIQFG..DDPF...WKEQQEVAD
Retrocopy KPYLPHIIQFGFADDPF<PSWKEQQEVAD

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	17.76 RPM
SRP017611_kidney	0.00 RPM	25.96 RPM
SRP017611_liver	0.00 RPM	18.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1118 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013286	1 retrocopy	retro_chof_1398,
Callithrix jacchus	ENSCJAG00000005170	1 retrocopy	retro_cjac_768,
Macaca mulatta	ENSMMUG00000004146	1 retrocopy	retro_mmul_2604,
Rattus norvegicus	ENSRNOG00000007972	1 retrocopy	retro_rnor_1118 ,