RetrogeneDB ID: retro_cjac_1530

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:94957027..94957363(-)
• Located in intron of: ENSCJAG00000015651

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSMB
• Ensembl ID: ENSCJAG00000013377
• Aliases: None
• Description: None

Sequence

>retro_cjac_1530
AATGTTCTCCTGGGCGGCCTTGTGTTCTTTGCCACCTTTGTGACTTTATGCAATGGATCATGCTATGTAATACGTCATAA
AATAGTTCCAGGAGAGACAATCAAAGAATGCACGGATCTCAAAGGAAACAAACACCCAATAGACTCAAGGTGGCGGACTG
AAGACTGTGAGCTATGTGCTTTCTGTGACATAGAAACATCATGTTGCTCCCTTGTTTCTACACCTGTGGGTTGTGACAGA
CACAACTGCCGGAAAATCTTCAACAAGGAGACCTGCAAGATAAGTGTGGTGGAGAAGAAGGACCCAAATAGGCCCTGTGG
TGTCAATGGATGGATA

Alignment

ORF - retro_cjac_1530 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVLLGGLVIFATFVTLCNASCYLIPNKMVPGDSNKECTDLKGNKHPLNSRWQTENCDECDCLEKEISCCS
          NVLLGGLV.FATFVTLCN.SCY.I..K.VPG...KECTDLKGNKHP..SRW.TE.C..C.....E.SCCS
Retrocopy NVLLGGLVFFATFVTLCNGSCYVIRHKIVPGETIKECTDLKGNKHPIDSRWRTEDCELCAFCDIETSCCS

Parental  LVAIPVGYDKDNCQKIFKQEDCKYIVVEKKDPNKTCDVSQWI
          LV..PVG.D..NC.KIF..E.CK..VVEKKDPN..C.V..WI
Retrocopy LVSTPVGCDRHNCRKIFNKETCKISVVEKKDPNRPCGVNGWI

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	0.80 RPM	1.60 RPM
SRP051959_heart	0.46 RPM	0.58 RPM
SRP051959_kidney	0.42 RPM	9.36 RPM
SRP051959_liver	0.28 RPM	1.82 RPM
SRP051959_lung	0.73 RPM	8.39 RPM
SRP051959_lymph_node	0.87 RPM	0.46 RPM
SRP051959_skeletal_muscle	0.20 RPM	0.13 RPM
SRP051959_spleen	0.76 RPM	1.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1530 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1530 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1530 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013377	1 retrocopy	retro_cjac_1530 ,
Cavia porcellus	ENSCPOG00000023456	1 retrocopy	retro_cpor_802,