RetrogeneDB ID: retro_rnor_2069

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:152109936..152110245(-)
• Located in intron of: ENSRNOG00000047851

Retrocopy information

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

Parental gene information

• Parental gene symbol: Selt
• Ensembl ID: ENSRNOG00000013507
• Aliases: None
• Description: selenoprotein T precursor [Source:RefSeq peptide;Acc:NP_001014275]

Sequence

>retro_rnor_2069
GTTTTTGGCCAATGCTATCCAGACATCTCTATGGAAGGAGAGAATTATCTCCCTCAACCAATCTATAGACACATAGCCTC
TTTCCTGTCAGTCTTTAACCTAGTATTAGTAGGTTTAATAATTGTTGGCAAAGATCTTTTTGCTTTTTTCAGCATGGAAG
CTCATAGCATCTGGCAGTGGGGGGGCCAAGAAAATAAGGATTATGCATGTATAATGTTTTTCTTCTTGAGAAACATGATT
GAGAACCAGTGTATGTGAACAGGTAGATTTGAGATAACTTTAAATTGTGTGCTGGTATGATCTAAGGTA

Alignment

ORF - retro_rnor_2069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 74.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VISQRYPDIRIEGENYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQW-GQENKVYAC
          V..Q.YPDI..EGENYLPQPIYRHIASFLSVF.LVL.GLIIVGKD.FAFF.M.A.SIWQW.GQENK.YAC
Retrocopy VFGQCYPDISMEGENYLPQPIYRHIASFLSVFNLVLVGLIIVGKDLFAFFSMEAHSIWQWGGQENKDYAC

Parental  MMVFFLSNMIENQCMSTGAFEITLNDVPVWSKL
          .M.FFL.NMIENQCM.TG.FEITLN.V.V.SK.
Retrocopy IMFFFLRNMIENQCM*TGRFEITLNCVLV*SKV

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	52.41 RPM
SRP017611_kidney	0.00 RPM	57.15 RPM
SRP017611_liver	0.00 RPM	45.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2069 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069 ,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,