RetrogeneDB ID: retro_cjac_2403

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:8533872..8534498(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000035497
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSCJAG00000000685
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_cjac_2403
GCCGGCCGCAGCATGGCTCACTGGCCCGGCGCGCTGATGCTCAAGTGAGTGGTGGTCGGCGACGGGGCGGTGGGCAAGAC
GTGCCTACTCATGAGCTATGCCAACGACGCCTTCCCGGAGGAGTACGTGCCCACCGTCTTCGACCACTACGCAGTCAGCG
TCACCGTGGGGGCAAGCAGTACCTCCTCGGACTCTACGACACGGCCGGACAGGAAGACTATGACCGTCTGAGGCCTTTAT
CTTACCCAGTGACCGACGTCTTCCTTATATGCTTCTCGGTGGTAAATCCAGCCTCATTTCAAAATGTGAAAGAGGAGTGG
GTACCGGAACTTAAGGAATACGCACCAAATGTACCCTTTTTATTAATAGGAACTCAGATTGATCTCCGAGATGACCCCAA
AACTTTAGCAAGACTGAATGATATGAAAGAAAAACCTATATGTGTGGAACAAGGACAGAAACTAGCAAAAGAGATAAGAA
CATGCTGCTATGTGGAATGTTCAGCTTTAACCCCGAAGGGATTGAAGACTGTTTTTGATGAGGCTATCATAGCCATTTTA
ACTCCAAAGAAACACACAGTAAAAAAAAGAATAGGATCAAGATGTATAAACTGTTGTTTAATTACA

Alignment

ORF - retro_cjac_2403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.67 %
• Parental protein coverage: 98.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGRSMAHGPGALMLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVG-GKQYLLGLYDTA
          AGRSMAH.PGALMLK.VVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVG.GKQYLLGLYDTA
Retrocopy AGRSMAHWPGALMLK*VVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVG<GKQYLLGLYDTA

Parental  GQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARL
          GQEDYDRLRPLSYP.TDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARL
Retrocopy GQEDYDRLRPLSYPVTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARL

Parental  NDMKEKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTVKKRIGSRCINCCLIT
          NDMKEKPICVEQGQKLAKEI..CCYVECSALT.KGLKTVFDEAIIAILTPKKHTVKKRIGSRCINCCLIT
Retrocopy NDMKEKPICVEQGQKLAKEIRTCCYVECSALTPKGLKTVFDEAIIAILTPKKHTVKKRIGSRCINCCLIT

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	15.69 RPM
SRP051959_heart	0.21 RPM	120.75 RPM
SRP051959_kidney	0.18 RPM	24.36 RPM
SRP051959_liver	0.02 RPM	9.34 RPM
SRP051959_lung	0.10 RPM	30.52 RPM
SRP051959_lymph_node	0.02 RPM	18.31 RPM
SRP051959_skeletal_muscle	0.22 RPM	117.73 RPM
SRP051959_spleen	0.08 RPM	36.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2403 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403 ,
Callithrix jacchus	ENSCJAG00000002144	4 retrocopies	retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,