RetrogeneDB ID: retro_mmus_360

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:122190220..122190913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gdi2
• Ensembl ID: ENSMUSG00000021218
• Aliases: Gdi2, GDI-B, GDIB, Gdi3
• Description: guanosine diphosphate (GDP) dissociation inhibitor 2 [Source:MGI Symbol;Acc:MGI:99845]

Sequence

>retro_mmus_360
ATGAGAGCTGTGTATAAGAAGTTTGATTTGGGCTAAGATGTTATAGACTTTACTGTCCATTCTCTTTTACTGTACAGAAC
AGATGATTTCTTAGATCAGCCATGTTGTGAAACCATTAATGGAATTAAACTTTACAGTGAGCCTTTGGCAAGATATAGTA
AAAGCCCATATCTCTAACCCCTTTATGGTCTTGGTGAGTTGCCCCAAGGATTTGCAAGGTTAAATGCTGTATATGGAGGT
ACCTACTTGTTGATAAACCAATTGAAAAAAATCACTGTGCAAAATGGAAAAGTGTTTGGCATAAAATCTGAGTTAGAGAT
TGTTCACTGTAAGCAGCTCATCTGTGATCCCAACTATGTAAAAGATCGGGTTGAAAAAATGGGCCAGGTAATCAGAGTGC
CCTGTATTCTTAGCCACCCTATAAAGAATAGCAATGATGCTAACTCCTGCTAGATCATCATTCCACAGAACCAAGTCAAT
GGCAAGTCAGATATCTATGTTTGCATGATCTCCTTTGCACATAATGTGGCAGCATATGGCAAGTATATTGCCATTGTAAG
TACAACTGTGGAGACCAAGGAACCAGAGAAAGAAATCCAACCAGATTTGCAGCTCTCTGAACCAATTGAACAGAAATTTG
TTAGCATCAATGACCTCTTTGTACCTAAAGCTTTGTGAACAGAGTCAGATATT

Alignment

ORF - retro_mmus_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 51.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRDVYKKFDLGQDVIDFTGHSLALYRTDDYLDQPCCETINRIKLYSESLARYGKSPYLYPLYGLGELPQG
          MR.VYKKFDLG.DVIDFT.HSL.LYRTDD.LDQPCCETIN.IKLYSE.LARY.KSPYL.PLYGLGELPQG
Retrocopy MRAVYKKFDLG*DVIDFTVHSLLLYRTDDFLDQPCCETINGIKLYSEPLARYSKSPYL*PLYGLGELPQG

Parental  FARLSAIYGGTYMLNKPIEEIIVQNGKVVGVKSEGEIARCKQLICDPSYVKDRVEKVGQVIRVICILSHP
          FARL.A.YGGTY.L......I.VQNGKV.G.KSE.EI..CKQLICDP.YVKDRVEK.GQVIRV.CILSHP
Retrocopy FARLNAVYGGTYLLINQLKKITVQNGKVFGIKSELEIVHCKQLICDPNYVKDRVEKMGQVIRVPCILSHP

Parental  IKNTNDANSCQIIIPQNQVNRKSDIYVCMISFAHNVAAQGKYIAIVSTTVETKEPEKEIRPALELLEPIE
          IKN.NDANSC.IIIPQNQVN.KSDIYVCMISFAHNVAA.GKYIAIVSTTVETKEPEKEI.P.L.L.EPIE
Retrocopy IKNSNDANSC*IIIPQNQVNGKSDIYVCMISFAHNVAAYGKYIAIVSTTVETKEPEKEIQPDLQLSEPIE

Parental  QKFVSISDLFVPKDLGTDSQI
          QKFVSI.DLFVPK.L.T.S.I
Retrocopy QKFVSINDLFVPKAL*TESDI

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	175.81 RPM
SRP007412_cerebellum	0.00 RPM	145.16 RPM
SRP007412_heart	0.00 RPM	121.69 RPM
SRP007412_kidney	0.04 RPM	243.41 RPM
SRP007412_liver	0.00 RPM	220.22 RPM
SRP007412_testis	0.05 RPM	192.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_360 was not detected

EST

No EST(s) were mapped for retro_mmus_360 retrocopy.

TSS

No TSS is located nearby retro_mmus_360 retrocopy 5' end.

Lab

retro_mmus_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360 ,
Mus musculus	ENSMUSG00000025531	1 retrocopy	retro_mmus_284,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,