RetrogeneDB ID: retro_cjac_4091

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:76564342..76565044(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUF2
• Ensembl ID: ENSCJAG00000004050
• Aliases: None
• Description: None

Sequence

>retro_cjac_4091
GTTTCTCTGAAAGAAATACAAGAGAATTTGAAAACAAAAATTGTGGATTCTCCAGAGAAGCTAAAGAATTATAAAGAAAA
AGTGAAAGATAAAGTCCAGAAGCTTAAAAATGCCAGGCAAGAAGTGGTAGAGAAATATGAACTCTATGGAGATTCAGTTG
ACTGCCTACCTTCATGTCAGTTGGAAGTGCAGTTATATCGAAAGAAAATACAGGACCTTTCAGATAATAAGGAAAAATTA
GCCAGTATCTTAAAGGAGAGCCTGAACTTGGAGGACCAAATTGAGAGTGGTGAGTCAGAACTGAAGAAATTGAAGACTGA
AGAAAATTCGTTCAAAAGACTGATGATTGTGAAGAAGGAAAAACTTGCCACAGTGCAGTTCAAAATAAATAAGAAGCACG
AAGATGTTAAGCAATACAAACGCACAGTAATTGAGGATTGCAATAAAGTTCAAGAAAAAAGAGGTGCTGTCTGTAAGCAA
GTAACCACAATTAATCAAGAAATCCAGAAATACAAATTTGAAATTCAGCAACTAAAAGATGCTACGGAAAGGGAGAAGCT
GAAGTTCCAGGAAATATTTTTAAACTTGAAAACTGCTTTGGAGAAATACCACGAAGGTATTGAAAAGGCCACAGAGGACT
CTTATGCTAAGATAGATGAGAAGACAGCTGAACTGAAGAGGAAGATGTTCAAAATGTCAACC

Alignment

ORF - retro_cjac_4091 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 50.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSLKEIQENLKTKIVDSPEKLKNYKEKMKDKVQKLKNARQEVVEKYELYGDSVDCLPSCQLEVQLYRKKI
          VSLKEIQENLKTKIVDSPEKLKNYKEK.KDKVQKLKNARQEVVEKYELYGDSVDCLPSCQLEVQLYRKKI
Retrocopy VSLKEIQENLKTKIVDSPEKLKNYKEKVKDKVQKLKNARQEVVEKYELYGDSVDCLPSCQLEVQLYRKKI

Parental  QDLSDNKEKLASILKESLNLEDQIESGESELKKLKTEENSFKRLMIVKKEKLATVQFKINKKHEDVKQYK
          QDLSDNKEKLASILKESLNLEDQIESGESELKKLKTEENSFKRLMIVKKEKLATVQFKINKKHEDVKQYK
Retrocopy QDLSDNKEKLASILKESLNLEDQIESGESELKKLKTEENSFKRLMIVKKEKLATVQFKINKKHEDVKQYK

Parental  RTVIEDCNKVQEKRGAVCKQVTTINQEIQKYKFEIQQLKDATEREKLKFQEIFLNLKTALEKYHEGIEKA
          RTVIEDCNKVQEKRGAVCKQVTTINQEIQKYKFEIQQLKDATEREKLKFQEIFLNLKTALEKYHEGIEKA
Retrocopy RTVIEDCNKVQEKRGAVCKQVTTINQEIQKYKFEIQQLKDATEREKLKFQEIFLNLKTALEKYHEGIEKA

Parental  TEDSYAKIDEKTAELKRKMFKMST
          TEDSYAKIDEKTAELKRKMFKMST
Retrocopy TEDSYAKIDEKTAELKRKMFKMST

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	0.33 RPM	3.22 RPM
SRP051959_heart	0.53 RPM	0.44 RPM
SRP051959_kidney	0.91 RPM	0.40 RPM
SRP051959_liver	0.32 RPM	0.43 RPM
SRP051959_lung	0.24 RPM	1.14 RPM
SRP051959_lymph_node	0.98 RPM	2.37 RPM
SRP051959_skeletal_muscle	0.46 RPM	0.15 RPM
SRP051959_spleen	0.48 RPM	1.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4091 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4091 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4091 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004050	1 retrocopy	retro_cjac_4091 ,
Macropus eugenii	ENSMEUG00000007093	1 retrocopy	retro_meug_1493,
Tupaia belangeri	ENSTBEG00000011027	1 retrocopy	retro_tbel_4643,