RetrogeneDB ID: retro_cjac_4210

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:105184983..105185592(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022501
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: WDYHV1
• Ensembl ID: ENSCJAG00000000865
• Aliases: None
• Description: WDYHV motif containing 1 [Source:HGNC Symbol;Acc:25490]

Sequence

>retro_cjac_4210
ATGGAGGGTAATGGCCCTGCTGCCACCCAGTACCAGCCGGCCAGCCCCCCGCAGGATGCCTGTGTCTACAGCAGCTGCTA
CTGTGAAGAAAATATTTGGAAGCTCTGTGAATACATCAAAAACCATGACCAGTATCCTTTAGAAGAATGTTATGCTGTCT
TCATATCTATTGAGAAGATGATCCCTATCTGGAAGCAACAGGCAAGACCTGGAGATGGACCTGTGATCTGGGATTACCAT
GTCGTTTTGCTTCATGTTTCAAGTGGAGGACAGAGCTTCATTTATGACCTCGATACTGTCTTGCTGTTTCCCTGCCCTAT
TGACACTTATGTAGAAGATGCCTTTAAGTCTGATGAAGACATTCATCCACAGTTTAAAAGGAAATTTAGAGTGATCCATG
CAGATTCATATTTGAAGAACTTTGCTTCTGACCAATGTCACATGAAAGACTCCAGTGGGAATTGGAGAGAGCCTCCTCTA
CCATATCCCTGCATTGAGACTGGAGATTCCAAAACAAACCTGAATGATTTCATCAGCATGGACCCCGAGGTAGGGTGGGG
CACTGTCTACACACTTTCTGAATTTACACATTGGTTTGGCAGTAAAAAC

Alignment

ORF - retro_cjac_4210 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.63 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGNGPAAAQYQPASPPRDACVYSSCYCEENIWKLCEYIKNHDQYPLEECYAVFISNERKMIPIWKQQAR
          MEGNGPAA.QYQPASPP.DACVYSSCYCEENIWKLCEYIKNHDQYPLEECYAVFIS.E.KMIPIWKQQAR
Retrocopy MEGNGPAATQYQPASPPQDACVYSSCYCEENIWKLCEYIKNHDQYPLEECYAVFISIE-KMIPIWKQQAR

Parental  PGDGPVIWDYHVVLLHVSSGGQSFIYDLDSVLPFPCPFDTYVEDAFKSDEDIHPQFRRKFRVIRADSYLK
          PGDGPVIWDYHVVLLHVSSGGQSFIYDLD.VL.FPCP.DTYVEDAFKSDEDIHPQF.RKFRVI.ADSYLK
Retrocopy PGDGPVIWDYHVVLLHVSSGGQSFIYDLDTVLLFPCPIDTYVEDAFKSDEDIHPQFKRKFRVIHADSYLK

Parental  NFASDRSHMKDSSGNWREPPPPYPCIETGDSKMNLNDFISMDPEVGWGTVYTLSEFTHWFGSKN
          NFASD..HMKDSSGNWREPP.PYPCIETGDSK.NLNDFISMDPEVGWGTVYTLSEFTHWFGSKN
Retrocopy NFASDQCHMKDSSGNWREPPLPYPCIETGDSKTNLNDFISMDPEVGWGTVYTLSEFTHWFGSKN

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	2.00 RPM
SRP051959_heart	0.02 RPM	3.79 RPM
SRP051959_kidney	0.00 RPM	4.88 RPM
SRP051959_liver	0.02 RPM	4.35 RPM
SRP051959_lung	0.00 RPM	2.93 RPM
SRP051959_lymph_node	0.00 RPM	2.72 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.62 RPM
SRP051959_spleen	0.00 RPM	3.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4210 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4210 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000865	1 retrocopy	retro_cjac_4210 ,
Macropus eugenii	ENSMEUG00000008130	3 retrocopies	retro_meug_1679, retro_meug_491, retro_meug_565,
Oryctolagus cuniculus	ENSOCUG00000014201	1 retrocopy	retro_ocun_266,