RetrogeneDB ID: retro_rnor_1999

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:181453314..181453597(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1559786
• Ensembl ID: ENSRNOG00000012724
• Aliases: None
• Description: UPF0587 protein C1orf123 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q498R7]

Sequence

>retro_rnor_1999
AAAAGTGCAAGCTGTGTGCATGGGAGAACTATTGAAATTTTGAGCAATATCATCAAATCTTACAATGCTGCAGACAATGA
GAAGTTCAAGACAGTATTAGAATTTGAGTGCTGGGGCCTTGAACCAGTTGATTTCCAGCCCCAGGCTGGGTTTGCTGCTG
AAGGTGTGGAGTCAGTGACAGTCTTCAGTGACATTAACCCACAAGAAAAAGGTCTGGACAGACTATGATAAAAAGGCTCA
GTCGTCTGTAGGGATCTTCGAGGTCACCTATCAGTTTGTGAAG

Alignment

ORF - retro_rnor_1999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 58.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KCKLCARENSIEILSSTIKSYNAEDNEKFKTIVEFECRGLEPVDFQPQAGFAAEGVESGTVFSDINLQEK
          K...C.....IEILS..IKSYNA.DNEKFKT..EFEC.GLEPVDFQPQAGFAAEGVES.TVFSDIN.QEK
Retrocopy KSASCVHGRTIEILSNIIKSYNAADNEKFKTVLEFECWGLEPVDFQPQAGFAAEGVESVTVFSDINPQEK

Parental  D-WTDYDEKTQESVGIFEVTHQFVK
          ..WTDYD.K.Q.SVGIFEVT.QFVK
Retrocopy G>WTDYDKKAQSSVGIFEVTYQFVK

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	24.01 RPM
SRP017611_kidney	0.00 RPM	17.72 RPM
SRP017611_liver	0.00 RPM	9.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1999 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999 , retro_rnor_2403, retro_rnor_2705,