RetrogeneDB ID: retro_rnor_1899

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:96411632..96412097(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004381
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rfk
• Ensembl ID: ENSRNOG00000022273
• Aliases: None
• Description: riboflavin kinase [Source:RefSeq peptide;Acc:NP_001014128]

Sequence

>retro_rnor_1899
ATGAGGAGCCTGCCGTTCTTCTGCCGAGGTCAGGTGGTGCGTGGCTTCGGCCGCGGCTCCAAGCAACTGGGCATCCCCAC
AGCTAATTTTCCTGAACAAGTAGTAGACAATCTTCCAGCTGATGTGTCCACTGGCATCTATTACGGCTGGGCCAGCGTTG
GGAGTGGAGAGGTCCATAAAATGGTGGTGAGCATAGGATGGAATCCATACTACAAGAATGTGAAGAAGTCCATGCAAACC
CATATCATCCATACCTTCAAAGAGGACTTTTATGGGGAGATTCTCAATGTGGCCATTGTTGGCTACCTCAGACCTGAAAA
GAACTTTGATTCTTTAGAGTCACTTATTTCTGCGATTCAAGGTGATATTGAAGAAGCTAAAAAACAACTGGATTTACCAG
AACATTTGAAACTCAAAGATGACAATTTCTCCCAAGTTTTTAAAAGCAAAATTATGAATGGCCAC

Alignment

ORF - retro_rnor_1899 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRSLPFFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADVSTGIYYGWASVGSGEVHKMVVSIGWNPY
          MRSLPFFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADVSTGIYYGWASVGSGEVHKMVVSIGWNPY
Retrocopy MRSLPFFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADVSTGIYYGWASVGSGEVHKMVVSIGWNPY

Parental  YKNVKKSMETHIIHTFKEDFYGEILNVAIVGYLRPEKNFDSLESLISAIQGDIEEAKKQLDLPEHLKLKD
          YKNVKKSM.THIIHTFKEDFYGEILNVAIVGYLRPEKNFDSLESLISAIQGDIEEAKKQLDLPEHLKLKD
Retrocopy YKNVKKSMQTHIIHTFKEDFYGEILNVAIVGYLRPEKNFDSLESLISAIQGDIEEAKKQLDLPEHLKLKD

Parental  DNFFQVSKSKIMNGH
          DNF.QV.KSKIMNGH
Retrocopy DNFSQVFKSKIMNGH

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	16.54 RPM
SRP017611_kidney	0.00 RPM	69.29 RPM
SRP017611_liver	0.00 RPM	26.02 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1899 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1899 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000031816	3 retrocopies	retro_cjac_2553, retro_cjac_4032, retro_cjac_654,
Erinaceus europaeus	ENSEEUG00000015769	1 retrocopy	retro_eeur_425,
Gorilla gorilla	ENSGGOG00000010358	1 retrocopy	retro_ggor_339,
Macropus eugenii	ENSMEUG00000000988	6 retrocopies	retro_meug_1179, retro_meug_1815, retro_meug_1922, retro_meug_2144, retro_meug_268, retro_meug_698,
Monodelphis domestica	ENSMODG00000001904	2 retrocopies	retro_mdom_1404, retro_mdom_194,
Mus musculus	ENSMUSG00000024712	1 retrocopy	retro_mmus_3439,
Oryctolagus cuniculus	ENSOCUG00000001622	1 retrocopy	retro_ocun_591,
Otolemur garnettii	ENSOGAG00000013120	5 retrocopies	retro_ogar_1435, retro_ogar_1475, retro_ogar_3257, retro_ogar_725, retro_ogar_735,
Pongo abelii	ENSPPYG00000019302	5 retrocopies	retro_pabe_1224, retro_pabe_1622, retro_pabe_1763, retro_pabe_217, retro_pabe_2289,
Rattus norvegicus	ENSRNOG00000022273	5 retrocopies	retro_rnor_1099, retro_rnor_1899 , retro_rnor_2212, retro_rnor_2828, retro_rnor_2863,
Sarcophilus harrisii	ENSSHAG00000015887	3 retrocopies	retro_shar_79, retro_shar_85, retro_shar_99,