RetrogeneDB ID: retro_cjac_2601

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:26557645..26557942(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000013012
• Aliases: None
• Description: None

Sequence

>retro_cjac_2601
ATCATGGCCAGGATGCTGGTGCAGACCATTCACGCAGGCACCCAGAAGCTCCAAGATGTTGAGGCCAAGCAGAAAGTTGA
AGAGAAGATGGTAGTTCCCTGCCACACCAGCTTTAGCATTTACCCTCCCATTCTAAAAGGAAACTGCTCTCTGAGGTAGG
CAAGAAAGAAATTTTGGGAGATCCCAATTGCACACATTAAAGCATCCTGCAGCAACACAGAGATCCAGATAATCTCTGCC
ACTAATCAACCTCTTGCCCATACTTCCTGTGGAACAGAGAAATTTCCAAATGTCAAG

Alignment

ORF - retro_cjac_2601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 51.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVARTAARTIHTGARQLQDAAAKQEVEEKSAAPRHTSFSIYPPIPGEESSLRWAGKKFEEIPIAHIKASY
          ..AR....TIH.G...LQD..AKQ.VEEK...P.HTSFSIYPPI.....SLR.A.KKF.EIPIAHIKAS.
Retrocopy IMARMLVQTIHAGTQKLQDVEAKQKVEEKMVVPCHTSFSIYPPILKGNCSLR*ARKKFWEIPIAHIKASC

Parental  NNTQIQVLSASNQPLAHASCGTEGFRNAR
          .NT.IQ..SA.NQPLAH.SCGTE.F.N..
Retrocopy SNTEIQIISATNQPLAHTSCGTEKFPNVK

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	0.00 RPM	4.24 RPM
SRP051959_heart	0.00 RPM	5.79 RPM
SRP051959_kidney	0.00 RPM	5.99 RPM
SRP051959_liver	0.00 RPM	5.07 RPM
SRP051959_lung	0.00 RPM	4.08 RPM
SRP051959_lymph_node	0.00 RPM	4.93 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.57 RPM
SRP051959_spleen	0.00 RPM	5.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2601 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2601 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013012	2 retrocopies	retro_cjac_2601 , retro_cjac_2989,
Felis catus	ENSFCAG00000014967	1 retrocopy	retro_fcat_282,
Homo sapiens	ENSG00000181991	1 retrocopy	retro_hsap_2458,
Gorilla gorilla	ENSGGOG00000015152	1 retrocopy	retro_ggor_1531,
Macaca mulatta	ENSMMUG00000013659	1 retrocopy	retro_mmul_637,
Nomascus leucogenys	ENSNLEG00000011441	1 retrocopy	retro_nleu_1902,
Ochotona princeps	ENSOPRG00000008247	1 retrocopy	retro_opri_540,
Pongo abelii	ENSPPYG00000006751	2 retrocopies	retro_pabe_1808, retro_pabe_2583,
Pan troglodytes	ENSPTRG00000007420	1 retrocopy	retro_ptro_1419,