RetrogeneDB ID: retro_cjac_3664

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01193355.1:2794..3301(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR83
• Ensembl ID: ENSCJAG00000005272
• Aliases: None
• Description: WD repeat domain 83 [Source:HGNC Symbol;Acc:32672]

Sequence

>retro_cjac_3664
ATGGCTTTCCCTGAGCCAAAGCCGCGGCCACCGGAGCTGCCGCAGAAACGGTTGAAGACTCTGGACTGCGGGCAAGGGGC
AGTGCCAGCCGTACGATTTAACGTGGATGGCAATTACTGCCTGGCGTGCGGCAGCGACAAGACCCTGAAACTGTGGAACC
CACTTCGGGGAACGCTGCTGCGGACGTACAGCGGCCACGGCTACGAGGTGCTGGATGCGGCCGGCTCCTTTGACAACAGC
CTCTGCTCCGGCGGCGGCGGAGACAAGGCGGTGGTCCTGTGGGATGTGGCATCGGGGCAGGTCGTGCGCAAATTCCGGGG
CCACGCAGGGAAGGTGAACACGGTGCAGTTTAATGAAGAGGCCACAGTTATCCCGTCCGGCTCTATTGATTCCAGTATCC
GCTGTTGGGACTGCCGCTCACGGAGGCCTGAGCCAGTGCAGACGCTGGATGAGGCCAGAGATGGCGTGTCCAGTGTGGAG
GTGTCAGACCACGAGATCCTGGCAGGG

Alignment

ORF - retro_cjac_3664 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.27 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFPEPKPRPPELPQKRLKTLDCGQGAVRAVRFNVDGNYCLTCGSDKTLKLWNPLRGTLLRTYSGHGYEV
          MAFPEPKPRPPELPQKRLKTLDCGQGAV.AVRFNVDGNYCL.CGSDKTLKLWNPLRGTLLRTYSGHGYEV
Retrocopy MAFPEPKPRPPELPQKRLKTLDCGQGAVPAVRFNVDGNYCLACGSDKTLKLWNPLRGTLLRTYSGHGYEV

Parental  LDAAGSFDNSSLCSGGGDKAVVLWDVASGQVVRKFRGHAGKVNTVQFNEEATVILSGSIDSSIRCWDCRS
          LDAAGSFDNS....GGGDKAVVLWDVASGQVVRKFRGHAGKVNTVQFNEEATVI.SGSIDSSIRCWDCRS
Retrocopy LDAAGSFDNSLCSGGGGDKAVVLWDVASGQVVRKFRGHAGKVNTVQFNEEATVIPSGSIDSSIRCWDCRS

Parental  RRPEPVQTLDEARDGVSSVKVSDHEILAG
          RRPEPVQTLDEARDGVSSV.VSDHEILAG
Retrocopy RRPEPVQTLDEARDGVSSVEVSDHEILAG

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	0.11 RPM	0.22 RPM
SRP051959_heart	0.02 RPM	0.26 RPM
SRP051959_kidney	0.04 RPM	0.49 RPM
SRP051959_liver	0.56 RPM	0.35 RPM
SRP051959_lung	0.44 RPM	0.37 RPM
SRP051959_lymph_node	0.50 RPM	0.84 RPM
SRP051959_skeletal_muscle	0.09 RPM	0.44 RPM
SRP051959_spleen	0.38 RPM	0.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3664 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3664 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	ENSCJAG00000005272	1 retrocopy	retro_cjac_3664 ,
Callithrix jacchus	ENSCJAG00000010123	1 retrocopy	retro_cjac_1,