RetrogeneDB ID: retro_mmus_1779

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:60507445..60507718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rheb
• Ensembl ID: ENSMUSG00000028945
• Aliases: None
• Description: Ras homolog enriched in brain [Source:MGI Symbol;Acc:MGI:97912]

Sequence

>retro_mmus_1779
AAGTCATCATAGACAATTCAGGTTGTTGACTGCTGATTTGTTGACTCATATGACCGAATCACAGAAAGCACTCCCCCAAA
GTCTATCCCGGTGAATGGATCAAGACTGCAGTCTTCAACTTGCAGATGCAGCTGGGCAGGAGGAATACCCTGTTTCCCTC
AGACATACTTCATAGAGATCAACTGATACGTTCTTGTGGATTGTTATAGCAAAGGTTTTGAAGTGACTAATGTTTCCTAT
GGCAAATTGTTGGATGTGGTGGAGAAAGTGCAA

Alignment

ORF - retro_mmus_1779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 50.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSSLTIQFVEGQFVDSYDPTIENTFTKLITVNG-QEYHLQLVDTAGQDEYSI-FPQTYSIDINGYILVYS
          KSS.TIQ.V...FVDSYD...E.T..K.I.VNG.Q...LQL.D.AGQ.EY...FPQTY.I.IN.Y.LV..
Retrocopy KSS*TIQVVDC*FVDSYDRITESTPPKSIPVNG>QDCSLQLADAAGQEEYPV<FPQTYFIEIN*YVLVDC

Parental  VTSIKSFEVIKVIHGKLLDMVGKVQ
          ....K.FEV..V..GKLLD.V.KVQ
Retrocopy YS--KGFEVTNVSYGKLLDVVEKVQ

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	64.55 RPM
SRP007412_cerebellum	0.04 RPM	60.75 RPM
SRP007412_heart	0.00 RPM	49.40 RPM
SRP007412_kidney	0.00 RPM	53.59 RPM
SRP007412_liver	0.00 RPM	34.55 RPM
SRP007412_testis	0.09 RPM	12.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1779 was not detected

EST

No EST(s) were mapped for retro_mmus_1779 retrocopy.

TSS

No TSS is located nearby retro_mmus_1779 retrocopy 5' end.

Lab

retro_mmus_1779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1779 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373,
Callithrix jacchus	ENSCJAG00000020414	1 retrocopy	retro_cjac_1694,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568, retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779 ,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,