RetrogeneDB ID: retro_cjac_4180

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:65732150..65732474(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010580
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021322
• Aliases: None
• Description: None

Sequence

>retro_cjac_4180
ATGAGTGGTGGAGGGACAGAGACCTCTGTGGGTTGTGAGGCCACCCTGGGCTGAGGCAGCAACAAGAGGGACTCCCTGGG
AACCGCGGGCTCTGTGCACCTCATTATCAAGGATCTTGGAGAAATTCATTCAAGGCTTTTGGATCACAGACCAGTTATTC
AAGGAGAAACTCGTTATTTTGTAAAAGAATTTGAAGAGAAACATGGTCTTTGAGAAATGCCTGTTCTTGAAAATTTGAAG
AATATAATCCATGAAACAAATGAACATACTCTTCCCAGATGTAGGGACAAAATGTGGGACAATCTCAGCCAAGTTCTCCA
GAGA

Alignment

ORF - retro_cjac_4180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 57.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGGATETPVGCEAAPGGGSKKRDSLGTASSAHLIIKDLGEIHSRLLDHRPVIQGETRYFVKEFEEKRGL
          MSGG.TET.VGCEA..G.GS.KRDSLGTA.S.HLIIKDLGEIHSRLLDHRPVIQGETRYFVKEFEEK.GL
Retrocopy MSGGGTETSVGCEATLG*GSNKRDSLGTAGSVHLIIKDLGEIHSRLLDHRPVIQGETRYFVKEFEEKHGL

Parental  REMRVLENLKNMIHETNEHTLPRCRDTMRDNLSHVLQR
          .EM.VLENLKN.IHETNEHTLPRCRD.M.DNLS.VLQR
Retrocopy *EMPVLENLKNIIHETNEHTLPRCRDKMWDNLSQVLQR

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	0.22 RPM	70.80 RPM
SRP051959_heart	0.96 RPM	33.55 RPM
SRP051959_kidney	0.27 RPM	46.06 RPM
SRP051959_liver	0.24 RPM	196.20 RPM
SRP051959_lung	0.81 RPM	34.58 RPM
SRP051959_lymph_node	0.16 RPM	44.95 RPM
SRP051959_skeletal_muscle	0.24 RPM	20.72 RPM
SRP051959_spleen	0.74 RPM	58.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4180 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4180 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002184	4 retrocopies	retro_chof_1163, retro_chof_2176, retro_chof_2312, retro_chof_663,
Callithrix jacchus	ENSCJAG00000021322	2 retrocopies	retro_cjac_1041, retro_cjac_4180 ,
Microcebus murinus	ENSMICG00000005966	1 retrocopy	retro_mmur_31,