RetrogeneDB ID: retro_cjac_1694

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:4357541..4357886(+)
• Located in intron of: ENSCJAG00000036768

Retrocopy information

• Ensembl ID: ENSCJAG00000020646
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHEB
• Ensembl ID: ENSCJAG00000020414
• Aliases: None
• Description: Ras homolog enriched in brain [Source:HGNC Symbol;Acc:10011]

Sequence

>retro_cjac_1694
TTTCCTCAGACATACTCCATAGATATTAATGGCTATATTCTTGTGTATCCTGTTACATCAATCAAAAGTTTTGAAGTGAT
TAAAGTTATCCATGGCAAATTGTTGGATATGGTGGGGAAAGTGCAAATACCTATTATGTTGGTTGGGAATAAGAAGGACC
TGCATATGGAAAGGGTGATCAGTTATGAAGAAGGGAAAGCTTTTGCAGAAACTTGGAATGCAGCTTTTTTGGAATCTTCT
GCTAAAGGAAATCAGACCACTGTTGATGTCTTTAGAAGGATAATTTTGGAGGCAGAGAAGATTGATGGAGCAGCTTCAAA
AGGCAAGTCTTCGTGCTCGGTGATG

Alignment

ORF - retro_cjac_1694 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.78 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAE
          FPQTYSIDINGYILVY.VTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKA.AE
Retrocopy FPQTYSIDINGYILVYPVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKAFAE

Parental  SWNAAFLESSAKENQTAVDVFRRIILEAEKIDGAASQGKSSCSVM
          .WNAAFLESSAK.NQT.VDVFRRIILEAEKIDGAAS.GKSSCSVM
Retrocopy TWNAAFLESSAKGNQTTVDVFRRIILEAEKIDGAASKGKSSCSVM

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
SRP051959_colon	0.07 RPM	43.38 RPM
SRP051959_heart	0.07 RPM	52.94 RPM
SRP051959_kidney	0.11 RPM	49.85 RPM
SRP051959_liver	0.06 RPM	32.10 RPM
SRP051959_lung	0.13 RPM	36.49 RPM
SRP051959_lymph_node	0.05 RPM	34.82 RPM
SRP051959_skeletal_muscle	0.09 RPM	47.06 RPM
SRP051959_spleen	0.04 RPM	41.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1694 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 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,
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,