RetrogeneDB ID: retro_mmus_715

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:55554939..55555409(+)
• Located in intron of: ENSMUSG00000000263

Retrocopy information

• Ensembl ID: ENSMUSG00000083363
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uxt
• Ensembl ID: ENSMUSG00000001134
• Aliases: Uxt, 0910002B17Rik
• Description: ubiquitously expressed transcript [Source:MGI Symbol;Acc:MGI:1277988]

Sequence

>retro_mmus_715
ATGATGATGACTCCCGCACAATGGGCCTTGGGAACTGTAGGAGAGAAAGTGCTGTGGTATGAGGCCTTCATCAGTGATAT
ACTGCAGCAAGATTTGAGGAAGGTGCTGGACCATTGAGACAAGGTAAATGATCAGCTGTTCTATACCATCAGGTGAGAAA
TGTCATTGAACCACTCTAGGGAACTAATCACCCAGAGTTACATGTGTGGGTGGATTTGGGCTGGAACATTTTTGTTGAGG
TAGTGATCCCAGATATTTCACATATCTATGTGTCTCTGGGATATGGCTTTTCCCCGGAGTTGACACTGGCTAAAGCTCTC
AAGTTCATTGGATGAGAGAGTTCTCTCCTCACAGAGCTTAGGATCAGCCTCACAAAGGACTCCATGAATGTCAAAGCCCA
GATCTGCAAGGTGCTAGGAGGACATAGAGAACTATAAGGCTGGCAGAACTCCCCAGAGCCATCTCCCCAC

Alignment

ORF - retro_mmus_715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRRALDTVGEKVLRYETFISDVLQRDLQKVLDHRDKVYEQLS-VYLQLRNVIERLQETNHSELYM
          M...P...AL.TVGEKVL.YE.FISD.LQ.DL.KVLDH.DKV..QL...Y.Q.RNVIE.L..TNH.EL..
Retrocopy MMMTPAQWALGTVGEKVLWYEAFISDILQQDLRKVLDH*DKVNDQLF<LYHQVRNVIEPL*GTNHPELHV

Parental  QVDLGCNFFVDTVVPDTSRIYVALGYGFFLELTLAEALKFIDRKSSLLTELSDSLTKDSMNIKAHIHMML
          .VDLG.N.FV..V.PD.S.IYV.LGYGF..ELTLA.ALKFI...SSLLTEL..SLTKDSMN.KA.I...L
Retrocopy WVDLGWNIFVEVVIPDISHIYVSLGYGFSPELTLAKALKFIG*ESSLLTELRISLTKDSMNVKAQICKVL

Parental  EGLRELQGLQNFPEPSPH
          .G.REL.G.QN.PEPSPH
Retrocopy GGHREL*GWQNSPEPSPH

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	2.27 RPM
SRP007412_cerebellum	0.00 RPM	1.82 RPM
SRP007412_heart	0.00 RPM	6.23 RPM
SRP007412_kidney	0.02 RPM	6.80 RPM
SRP007412_liver	0.00 RPM	4.86 RPM
SRP007412_testis	0.00 RPM	1.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_715 was not detected

EST

No EST(s) were mapped for retro_mmus_715 retrocopy.

TSS

No TSS is located nearby retro_mmus_715 retrocopy 5' end.

Lab

retro_mmus_715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_715 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_683

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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,