RetrogeneDB ID: retro_cjac_2715

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:45049683..45049976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HN1
• Ensembl ID: ENSCJAG00000014553
• Aliases: None
• Description: None

Sequence

>retro_cjac_2715
ACTGCCACCGCCACCATCAAGGGTGTTGACTTCAACAGCAGGAATAGCTCCTGGGTTTTGTAGCTGCCAAGTGTGGATCC
AATTTTCCGTTGGGTTTTAATGAACCATCAGAACAACCTGTGAGAAAAGAACAAAATGGCTTCTAATATCTTTGGGACAC
CTGAAGAAAATCCACCTTCTTGGGCCACGTCAGCAGGTGCCAAGTCTAGAGGTGGTGGGGAAGACTTGAAGTCATCTGGA
CTGCAGGGAAGGAACTCTTCTGCTACTTACTCTGCAGATTCTTAGATCTGAAG

Alignment

ORF - retro_cjac_2715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTTTTFKGVDPNSRNSSRVLRPPGG-GSNFSLGFDEPTEQPVRK-NKMASNIFGTPEENQASWAKSAGAK
          T.T.T.KGVD.NSRNSS.VL..P...GSNF.LGF.EP.EQPVRK.NKMASNIFGTPEEN..SWA.SAGAK
Retrocopy TATATIKGVDFNSRNSSWVL*LPSV<GSNFPLGFNEPSEQPVRK>NKMASNIFGTPEENPPSWATSAGAK

Parental  SSGGREDLESSGLQRRNSSEASSGD-FLDLK
          S.GG.EDL.SSGLQ.RNSS...S.D.FLDLK
Retrocopy SRGGGEDLKSSGLQGRNSSATYSAD<FLDLK

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	9.07 RPM
SRP051959_heart	0.00 RPM	1.21 RPM
SRP051959_kidney	0.00 RPM	1.82 RPM
SRP051959_liver	0.00 RPM	2.58 RPM
SRP051959_lung	0.00 RPM	4.49 RPM
SRP051959_lymph_node	0.00 RPM	9.63 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.73 RPM
SRP051959_spleen	0.00 RPM	6.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2715 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2715 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2343
Pan troglodytes	retro_ptro_1715
Gorilla gorilla	retro_ggor_1780

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715 ,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647, retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449,