RetrogeneDB ID: retro_mmus_3109

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:16581823..16582500(+)
• Located in intron of: ENSMUSG00000060924

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdk4
• Ensembl ID: ENSMUSG00000006728
• Aliases: None
• Description: cyclin-dependent kinase 4 [Source:MGI Symbol;Acc:MGI:88357]

Sequence

>retro_mmus_3109
TCTGAAATTGCTGTTAGTACCTATGGAATGGTTTGGAAGGCCCGAGATTCCGACAATGGCCATGTTGAGGCCCTCAAGAT
TATGAGGGTTCCTAATGGAAGAGGATCTGAAGGGGGTCTTCCCATCAATACAGCTCATGAGGTAGCCTTACTTAGAAGAC
TGGAGGACTTAGAATATCCCAATGTTGTTCAGCTAAAGCACATCTGTAGTACTTCCTGAACTGACTGAGACAATAGGGTC
ATGGTAGTGTTTAAGAATATAGACTAGTACCTAAAGAAATACCTGGACAAAGCACCCCACACCCACCCCAGGCTTCCAAG
TTGAGATCATCAAGGACCTGTTGAAACAGTTTGTAAGCAGCCTGAATTTTCTTGATGCTAATTGTATTGTTCACCAAGAC
CTCAAATTAGGTTACATTCTGGTGACGAGTACTGGAACAGTCAAGATGGCTGACTTTGTCTTAGCCAGATTCTACAGCTA
CTGGATGTCTCCTCACACCCATGGCTGTTATATGCCAGTACTTTATTCCTCAAGTTCATCTGCAGTCTACATGTGTGACA
TCTGTGGACAAGTGGCATGTCCACTGTATCTTTGCTGAGATGTCTCACTGAATTCATCTCTTTCCTGGAAGCCAAGAGGC
TGAGCAGTTGGATAAAATCTTTGTTCTCATTGGATTG

Alignment

ORF - retro_mmus_3109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.35 %
• Parental protein coverage: 82.29 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGAAGGGLPVSTVREVALLRRLEAFEHPNVVRLMDVCA
          .EI.V..YG.V.KARD...GH..ALK..RVPNG....GGLP..T..EVALLRRLE..E.PNVV.L...C.
Retrocopy SEIAVSTYGMVWKARDSDNGHVEALKIMRVPNGRGSEGGLPINTAHEVALLRRLEDLEYPNVVQLKHICS

Parental  TSRTDRDIKVTLVFEHIDQDLRTYLDKAP--PPGLP-VETIKDLMRQFLSGLDFLHANCIVHRDLKPENI
          TS.TD.D..V..VF..ID..L..YLDKAP...P.LP.VE.IKDL..QF.S.L.FL.ANCIVH.DLK...I
Retrocopy TS*TD*DNRVMVVFKNID*YLKKYLDKAPHTHPRLP>VEIIKDLLKQFVSSLNFLDANCIVHQDLKLGYI

Parental  LVTSNGTVKLADFGLARIYSYQMA-LTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFC
          LVTS.GTVK.ADF.LAR.YSY.M..LTP..V...Y..P.V.LQST..T.VD.W.V.CIFAEM.....LF.
Retrocopy LVTSTGTVKMADFVLARFYSYWMS>LTPMAVICQYFIPQVHLQSTCVTSVDKWHVHCIFAEMSH*IHLFP

Parental  GNSEADQLGKIFDLIGL
          G..EA.QL.KIF.LIGL
Retrocopy GSQEAEQLDKIFVLIGL

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	0.09 RPM	26.35 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.00 RPM	26.06 RPM
SRP007412_kidney	0.00 RPM	35.73 RPM
SRP007412_liver	0.00 RPM	21.57 RPM
SRP007412_testis	0.00 RPM	15.92 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3109 was not detected

EST

No EST(s) were mapped for retro_mmus_3109 retrocopy.

TSS

No TSS is located nearby retro_mmus_3109 retrocopy 5' end.

Lab

retro_mmus_3109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Canis familiaris	ENSCAFG00000000280	1 retrocopy	retro_cfam_690,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Felis catus	ENSFCAG00000029663	1 retrocopy	retro_fcat_516,
Gorilla gorilla	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Microcebus murinus	ENSMICG00000003789	1 retrocopy	retro_mmur_893,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,
Macaca mulatta	ENSMMUG00000023694	1 retrocopy	retro_mmul_401,
Mus musculus	ENSMUSG00000006728	5 retrocopies	retro_mmus_1219, retro_mmus_1298, retro_mmus_2878, retro_mmus_3109 , retro_mmus_636,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pan troglodytes	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Tarsius syrichta	ENSTSYG00000011937	3 retrocopies	retro_tsyr_1383, retro_tsyr_1701, retro_tsyr_544,