RetrogeneDB ID: retro_mmus_1030

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:69549196..69549736(+)
• Located in intron of: ENSMUSG00000021595

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rabggtb
• Ensembl ID: ENSMUSG00000038975
• Aliases: None
• Description: RAB geranylgeranyl transferase, b subunit [Source:MGI Symbol;Acc:MGI:99537]

Sequence

>retro_mmus_1030
GATACTGGGAAAAAAATTGATACAAGATCCTCATTTTCTACAGTTGCAACTTCGGCTCTTTTAGGCAAGCTTGATGTGGG
ACAGGTAGCTGAATTCGTTTTGTCCTGTGTGAACTTTGATGATGGACTCGGTGTAGACTGGGCCCTGAATCTCATGCTGG
GTAGATCTACTCTTACACAAGATTCCTGCCAATGAGAACCAGTCAGTTGCATCAAGGGAATTCGGACTTACATGGTTGGT
GGCTTTGCGAATAATGGTTGGCTCAGGTGGACTCAATAGAAGACAGGAGAAGTTACCAGTTTCATGCTTTTTGTGGTTGG
GCTTGGCCTCAGTGCAGGTAATAGGGAGGCTTCCTCAGATTGATAGAGAAAAGCGGCGTGGCCTCACGTCTCCTTGAAGA
GGCTGGGGGGCTGGCAGGGAGGCCAGGAGATATGGTCCTTTACACAATTTATTCCGCATCGCTGGATTAACACCGCTGGG
AGAAGAACGGATGAGCCTGTTAGTGCTGCCTTCTGCATGCCTGAAAGCGTGGCTCAGAGG

Alignment

ORF - retro_mmus_1030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.59 %
• Parental protein coverage: 55.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFG-CRPGSESHAGQIYCCTGFLAI-
          D....IDTR.SF..VAT.ALLGKLD...V....EFVLSC.NFD.G.G.CR.G.ESHAG.IY..T.FL...
Retrocopy DTGKKIDTRSSFSTVATSALLGKLD---VGQVAEFVLSCVNFDDGLG<CRLGPESHAG*IYSYTRFLPMR

Parental  TSQLHQVNSDLLGWWLCERQLP-SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQD
          TSQLHQ.NSDL.GWWLCE..L..SGGLN.R.EKLP..C..W..LAS...IGRL..IDREK.R........
Retrocopy TSQLHQGNSDLHGWWLCE*WLA<SGGLNRRQEKLPVSCFLWLGLASVQVIGRLPQIDREKRRGLTSP*RG

Parental  EETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQI-KPVSPVFCMPEEVLQR
          ...G..A.R.G......H.LF.IAGL..LGEE....PVS..FCMPE.V.QR
Retrocopy WGAGREARRYGPL----HNLFRIAGLTPLGEERM<EPVSAAFCMPESVAQR

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	36.91 RPM
SRP007412_cerebellum	0.04 RPM	46.03 RPM
SRP007412_heart	0.00 RPM	48.16 RPM
SRP007412_kidney	0.00 RPM	52.34 RPM
SRP007412_liver	0.00 RPM	31.08 RPM
SRP007412_testis	0.00 RPM	7.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1030 was not detected

EST

No EST(s) were mapped for retro_mmus_1030 retrocopy.

TSS

No TSS is located nearby retro_mmus_1030 retrocopy 5' end.

Lab

retro_mmus_1030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1030 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030 ,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,