RetrogeneDB ID: retro_mmus_3439

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:36620182..36620459(+)
• Located in intron of: ENSMUSG00000059708

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rfk
• Ensembl ID: ENSMUSG00000024712
• Aliases: Rfk, 0610038L10Rik, AF031381, KOI-4
• Description: riboflavin kinase [Source:MGI Symbol;Acc:MGI:1914688]

Sequence

>retro_mmus_3439
TCCACTGGCACTTATTATAGTTTCTCTGGTGTTGGAAGTGAGAATGCCCATAAGATGGTGGTGAACACAAGGCTGGAACC
CATAGCGTAGGAATGTGAAAAAGTCCAGAGAATCACATATCATGTATACCTTCAAAGAGGACTTTTATGAGGAAATCCTC
TATGTGGCCGTTGTTGCCTACCTTGGCCCAGAAAAGAACTTTGATTCGTTAGTACCACTTATTTCAGTAACTCATGAGAT
TGAAGAAACAACTAAATGACTAGATTTACCACAATAT

Alignment

ORF - retro_mmus_3439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STGIYYGWASVGSGDVHKMVVSI-GWNPYYKNVKKSMETHIIHTFKEDFYGEILNVAIVGYLRPEKNFDS
          STG.YY....VGS...HKMVV...GWNP...NVKKS.E.HI..TFKEDFY.EIL.VA.V.YL.PEKNFDS
Retrocopy STGTYYSFSGVGSENAHKMVVNT>GWNP*RRNVKKSRESHIMYTFKEDFYEEILYVAVVAYLGPEKNFDS

Parental  LESLISAIQGDIEEAKKQLDLPEH
          L..LIS.....IEE..K.LDLP..
Retrocopy LVPLIS-VTHEIEETTK*LDLPQY

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
SRP007412_brain	0.00 RPM	44.13 RPM
SRP007412_cerebellum	0.13 RPM	46.94 RPM
SRP007412_heart	0.00 RPM	47.44 RPM
SRP007412_kidney	0.00 RPM	93.51 RPM
SRP007412_liver	0.00 RPM	42.77 RPM
SRP007412_testis	0.05 RPM	18.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3439 was not detected

EST

No EST(s) were mapped for retro_mmus_3439 retrocopy.

TSS

No TSS is located nearby retro_mmus_3439 retrocopy 5' end.

Lab

retro_mmus_3439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3439 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2863

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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,