RetrogeneDB ID: retro_mmus_3647

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:79631164..79631874(-)
• Located in intron of: ENSMUSG00000046942

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hdgf
• Ensembl ID: ENSMUSG00000004897
• Aliases: Hdgf, AI118077, D3Ertd299e
• Description: hepatoma-derived growth factor [Source:MGI Symbol;Acc:MGI:1194494]

Sequence

>retro_mmus_3647
ATGTCACGATCCAAGCAGCAGAAAGATCACTTTGCGAGGGACCTGGTGTTTGCAAAGATGAAGGGATACCAACATTTGCC
AGCCCGGATTGATGAGATGCCTGAGGCTGCAGTGAAGTCAACAGCCAACAAATACCAAATCTTTGGTGGGGGGGGCATGA
GACGGTATTCCTGGGCCCCAAAGACCTCTTCCCTTATGAGGAATCCAAGGAGAAGTTTGGCAAGCCCAACAAGGGGAAAG
GGTTCAGTGAGGGGCTGTGGGAGATCAAGAACAACCTACAGTTAGGGCCTCTGGCTACCAGTCCTCCCAGAAAAAGAGTT
GTGCGGCAGAGCCCGAGGTGGAGTCCGAAGCTCATGAGGGTGACAGTGACAAGAAGGGCAGTGCAGAGGGCAGCAGCAAC
GAAGAAGGGAAGCTGGTCATCGATGAGCCAGCCAAGGAGAAGAACAAAAAGGGCACAGCACGCTGAAGAGGAGAGCAGAG
GATGTGTTGGAGGACTCCCCTAAACGTCCCAAGGAGTCAGGAGACCATGAGGAGGAAAACAAGAAGATAGCTGCCATGGA
GGGTGAGAGGCCCCTGCCTGTAGAGATGGAGAAGAACAGCACCCCCTCTGAGCAAGACTCTGGCCAGGGACCTCTTGCAA
AAGAAGAAGGGAGGAAGAGGCTGCCAAGGAAGATGCTGAAGCCCAGGGCATCAGGGATCATGAGAGCCTG

Alignment

ORF - retro_mmus_3647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSRSNRQKEYKCGDLVFAKMKGYPHWPARIDEMPEAAVKSTANKYQVF-FFGTHETAFLGPKDLFPYEES
          MSRS..QK.....DLVFAKMKGY.H.PARIDEMPEAAVKSTANKYQ.F.....HET.FLGPKDLFPYEES
Retrocopy MSRSKQQKDHFARDLVFAKMKGYQHLPARIDEMPEAAVKSTANKYQIF<WXXXHETVFLGPKDLFPYEES

Parental  KEKFGKPNKRKGFSEGLWEIENN-PTVKASGYQSSQKKSCAAEPEVEPEAHEGDGDKKGSAEGSSDEEGK
          KEKFGKPNK.KGFSEGLWEI.NN.PTV.ASGYQSSQKKSCAAEPEVE.EAHEGD.DKKGSAEGSS.EEGK
Retrocopy KEKFGKPNKGKGFSEGLWEIKNN<PTVRASGYQSSQKKSCAAEPEVESEAHEGDSDKKGSAEGSSNEEGK

Parental  LVIDEPAKEKN-EKG--TLKRRAGDVLEDSPKRPKESGDHEEEDKEIAALEGERPLPVEVEKNSTPSEPD
          LVIDEPAKEKN..KG..TLKRRA.DVLEDSPKRPKESGDHEEE.K.IAA.EGERPLPVE.EKNSTPSE.D
Retrocopy LVIDEPAKEKN<QKGHSTLKRRAEDVLEDSPKRPKESGDHEEENKKIAAMEGERPLPVEMEKNSTPSEQD

Parental  SGQGPPAEEE-EGEEEAAKEEAEAQGVRDHESL
          SGQGP.A.EE...EE.AAKE.AEAQG.RDHESL
Retrocopy SGQGPLAKEE<REEE-AAKEDAEAQGIRDHESL

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	0.05 RPM	104.11 RPM
SRP007412_cerebellum	0.00 RPM	140.60 RPM
SRP007412_heart	0.03 RPM	122.59 RPM
SRP007412_kidney	0.10 RPM	182.58 RPM
SRP007412_liver	0.05 RPM	180.62 RPM
SRP007412_testis	0.50 RPM	293.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3647 was not detected

EST

No EST(s) were mapped for retro_mmus_3647 retrocopy.

TSS

No TSS is located nearby retro_mmus_3647 retrocopy 5' end.

Lab

retro_mmus_3647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3647 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039793	1 retrocopy	retro_btau_216,
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338, retro_cjac_4022,
Dasypus novemcinctus	ENSDNOG00000010231	1 retrocopy	retro_dnov_4,
Equus caballus	ENSECAG00000011178	1 retrocopy	retro_ecab_5,
Echinops telfairi	ENSETEG00000005243	1 retrocopy	retro_etel_1899,
Homo sapiens	ENSG00000143321	1 retrocopy	retro_hsap_33,
Myotis lucifugus	ENSMLUG00000010413	1 retrocopy	retro_mluc_257,
Mus musculus	ENSMUSG00000004897	1 retrocopy	retro_mmus_3647 ,
Mus musculus	ENSMUSG00000028484	1 retrocopy	retro_mmus_2896,
Pongo abelii	ENSPPYG00000000703	1 retrocopy	retro_pabe_6,
Pan troglodytes	ENSPTRG00000001474	1 retrocopy	retro_ptro_1,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65,