RetrogeneDB ID: retro_rnor_522

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:207970151..207970413(+)
• Located in intron of: ENSRNOG00000024414

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uxt
• Ensembl ID: ENSRNOG00000009893
• Aliases: None
• Description: Protein UXT [Source:UniProtKB/Swiss-Prot;Acc:Q63ZY7]

Sequence

>retro_rnor_522
ATGGAGAGGCCTCCAAAATGTTGGGCCTTAGATACTGTGAGGGAGAAAGAACTATGGTACATGGCCTGTATCAGTGACAT
ACTGCAGTGAGACTTGCAGAAGGCACTGGACCGTCAAAAACACTGTAAACAAGCAGTTGTCTATACTGAGAAATGTCATC
CAGAGACTCTGGGAAACTAATTACTCAAAGTTACATATGCAAGTGGATTAGGGAGGCAGCTTCCTTGGTGAAATGGTAGT
CCCAGATACTTCACACATGTGG

Alignment

ORF - retro_rnor_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 57.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRRALDTVGEKVLRYEAFISDVLQRDLQKVLDH-RDKVYEQLSVYLQLRNVIERLQETNHSELYM
          M..PPK..ALDTV.EK.L.Y.A.ISD.LQ.DLQK.LD.....V..QLS....LRNVI.RL.ETN.S.L.M
Retrocopy MERPPKCWALDTVREKELWYMACISDILQ*DLQKALDR>KNTVNKQLSI---LRNVIQRLWETNYSKLHM

Parental  QVDLGCNFFVDTMVPDTSRIY
          QVD.G..F.....VPDTS...
Retrocopy QVD*GGSFLGEMVVPDTSHMW

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	9.27 RPM
SRP017611_kidney	0.00 RPM	16.96 RPM
SRP017611_liver	0.00 RPM	10.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_522 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009154	1 retrocopy	retro_cpor_1302,
Dipodomys ordii	ENSDORG00000001025	1 retrocopy	retro_dord_627,
Erinaceus europaeus	ENSEEUG00000006151	1 retrocopy	retro_eeur_543,
Macropus eugenii	ENSMEUG00000003352	1 retrocopy	retro_meug_59,
Microcebus murinus	ENSMICG00000016263	1 retrocopy	retro_mmur_1156,
Mustela putorius furo	ENSMPUG00000013405	1 retrocopy	retro_mputfur_999,
Mus musculus	ENSMUSG00000001134	3 retrocopies	retro_mmus_1424, retro_mmus_1766, retro_mmus_715,
Rattus norvegicus	ENSRNOG00000009893	5 retrocopies	retro_rnor_521, retro_rnor_522 , retro_rnor_683, retro_rnor_692, retro_rnor_882,
Tarsius syrichta	ENSTSYG00000012719	2 retrocopies	retro_tsyr_237, retro_tsyr_778,