RetrogeneDB ID: retro_mmus_1394

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:47699713..47700526(-)
• Located in intron of: ENSMUSG00000022311

Retrocopy information

• Ensembl ID: ENSMUSG00000089828
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Wdr12
• Ensembl ID: ENSMUSG00000026019
• Aliases: Wdr12, 4933402C23Rik, Ytm1, Ytm1p
• Description: WD repeat domain 12 [Source:MGI Symbol;Acc:MGI:1927241]

Sequence

>retro_mmus_1394
GACAGTTTGTCCTGCTTACTACAGACTGTCTCAATGGAGCAGACTATTCTCTAATAGGAGTGGAACATTGAGAAGACCAA
AGTGAAAGCTCTGTAATGCTGCCAAGGGCATGATGGGAGTGTGGATGCCATAGTAGTCAATAGCTTTAGCTTAGGAACTA
AGTTTTGCAGTGACTCCTGGGATAAGATGCTAAAGATCTGGTCTACAGTCCCTATTGATGAAGAAGATTAAATGGAAGAA
CCCACAAATCGACTAAGAAAAAAAAAAAAAAAGAACAATTGGGACTAACAAGAACACCCTTTGTGACCCTCTCTGGCCAC
ACAGAAGCAATTTCCTCAGTCTTTTGGACAGATTCTGAAGAACTCTGTAGTTGGAATTACACAATTAAGAGTGTGGGATG
TTGAGTCTGGTGGTCTTAAGTCAACTGTGACAGGAAATAAAGTGTTTAATTCTATCTTCTATTCTTGCCTTTGTAAATGT
TTGGCATCTGGAAGTATAGACAGGCATATTAGACTATGGGATCCCGGAACTAAAGATGGTTCTTTGGTGTCGATGTCTCT
CACCTCACACACAGGCTGGGTGACATCAGTGACGTAGTCTCCTACCCATGAACAGCAGCTGGTCTCAGGCTGGTTAGATA
ACATTGTGAAGCTATGGGATACAAGAAGTTGTAAGGTTTCTCTCTATGATCTAGCTGCTCATGAAGACAAAGTTCTACGT
GTGGATTGGACAGACACAGGGATATTTTTGAGTGGAGGAACAGACAATAAATTGTATTCCTACAGATATTCCCCTAGTAC
TTCCGATGTGGGG

Alignment

ORF - retro_mmus_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.18 %
• Parental protein coverage: 64.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSLSCLLLTASMDQTVLLWEWNVEKNKVKALHCCRGHAGSVDAIAVDSS--GAKFCSGSWDKMLKIWSTV
          DSLSCLL.T.SM.QT.L..EWN.EK.KVKAL.CC.GH.GSVDAI.V.S...G.KFCS.SWDKMLKIWSTV
Retrocopy DSLSCLLQTVSMEQTIL**EWNIEKTKVKAL*CCQGHDGSVDAIVVNSFSLGTKFCSDSWDKMLKIWSTV

Parental  PTDEEDEMEEATNR-PRKKQKTEQLGLTRTPLVTLSGHTEAISSVLWSDAEEICSASWDHTI-RVWDVES
          P.DEED.MEE.TNR........EQLGLTRTP.VTLSGHTEAISSV.W.D.EE.CS..W..TI.RVWDVES
Retrocopy PIDEED*MEEPTNR<TKXXXXXEQLGLTRTPFVTLSGHTEAISSVFWTDSEELCS--WNYTI>RVWDVES

Parental  GGLKSTLTGNKVFNCISYSPLCKRLASGSTDRHIRLWDPRTKDGSLVSLSLTSHTGWVTSVKWSPTHEQQ
          GGLKST.TGNKVFN.I.YS.LCK.LASGS.DRHIRLWDP.TKDGSLVS.SLTSHTGWVTSV..SPTHEQQ
Retrocopy GGLKSTVTGNKVFNSIFYSCLCKCLASGSIDRHIRLWDPGTKDGSLVSMSLTSHTGWVTSVT*SPTHEQQ

Parental  LISGSLDNIVKLWDTRSCKAPLYDLAAHEDKVLSVDWTDTGLLLSGGADNKLYSYSYSPTTSHVG
          L.SG.LDNIVKLWDTRSCK..LYDLAAHEDKVL.VDWTDTG..LSGG.DNKLYSY.YSP.TS.VG
Retrocopy LVSGWLDNIVKLWDTRSCKVSLYDLAAHEDKVLRVDWTDTGIFLSGGTDNKLYSYRYSPSTSDVG

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	0.02 RPM	26.05 RPM
SRP007412_cerebellum	0.00 RPM	20.19 RPM
SRP007412_heart	0.00 RPM	11.02 RPM
SRP007412_kidney	0.00 RPM	12.32 RPM
SRP007412_liver	0.00 RPM	11.55 RPM
SRP007412_testis	0.00 RPM	111.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1394 was not detected

EST

No EST(s) were mapped for retro_mmus_1394 retrocopy.

TSS

No TSS is located nearby retro_mmus_1394 retrocopy 5' end.

Lab

retro_mmus_1394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1394 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394 , retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,