RetrogeneDB ID: retro_cjac_2612

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:51907113..51907483(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000019082
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAL
• Ensembl ID: ENSCJAG00000015858
• Aliases: None
• Description: None

Sequence

>retro_cjac_2612
ATGGCTCGAGGCAGCGCCCTCCTGCTCGCCTCCCTCCTCCTCGCCGCCGCCTTTTCTGCCTCTGAGGGGCTCTGGTCGCC
GGACAAAGAAAAACCGAGGCTGGACCCTGAACAGCGCGGGCTACCTGCTGGGCCAACATGCCGTTGGCAACTACAGATCA
TTCAGCGACAAGCTTGGCTTCACCAGCAAGCGGGAGATGCAGCCTGAAGATGAGGTGAAACCAGGTAGCTTTGATAGGTC
CACCGCTGAGAGCAACGTTGTGCGCACGATCGTTGAGTTCCTGTCTTTCCTGCATCTCAAAGAGACCGGGACCCTCGACG
GCCTCCCTGATGTCCCGGCCGTAGCCTCCCTGGATGAAACCGAGCGTTCC

Alignment

ORF - retro_cjac_2612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARGSALLLASLLLAVAFSASAGFWSPLKAKEKRGWTLNSAGYLLGP-HAVGNHRSFSDKLGLTSKREMQ
          MARGSALLLASLLLA.AFSAS.G.WSP...KEK........G...GP.HAVGN.RSFSDKLG.TSKREMQ
Retrocopy MARGSALLLASLLLAAAFSASEGLWSP--DKEKPRLDPEQRGLPAGP>HAVGNYRSFSDKLGFTSKREMQ

Parental  PEDEVKPGSFDWSTAESNVVRTIVEFLSFLHLKEAGALDGLPDVRAAASLDDTERS
          PEDEVKPGSFD.STAESNVVRTIVEFLSFLHLKE.G.LDGLPDV.A.ASLD.TERS
Retrocopy PEDEVKPGSFDRSTAESNVVRTIVEFLSFLHLKETGTLDGLPDVPAVASLDETERS

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	0.02 RPM	0.22 RPM
SRP051959_heart	0.00 RPM	0.04 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.02 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2612 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015858	1 retrocopy	retro_cjac_2612 ,