RetrogeneDB ID: retro_cjac_3153

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:81170245..81170752(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000016922
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFAF2
• Ensembl ID: ENSCJAG00000015375
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 2 [Source:HGNC Symbol;Acc:28086]

Sequence

>retro_cjac_3153
ATGCGTTGGTCTCAGGATTTGTTCCGCTTCTTGTGGAGATCGCTGTCACGGGAGGTGAAGGAGCACGTGGGCACCGACCA
GTTCGGGAACAAATACTACTATATCGCGGGGTACAAGAACTGGAGAGGACAAACTATTCGAGAGAAAAGAATTGTAGAAG
CAGCAAAAAAACAAGAAGTAGACTATGAACCAGGGGATATTCCTACAGAATGGGAAGCTTGGATTAGAAGAACAAGAAAG
ACTCCACCTACTATGGAGGAAATACTAAAGAATGAAAAATACAGAGAAGAAATCAAAATAAAAAGCCGAGAGTTTTATGA
AAAAGAAAAAGTCCTTAGTAAAGAGACCAATGAAGAACTCTTGGCTCCACCAGCTGACACTCAAATTAAAGGACATGCCT
CTGCTCCATACTTTGGAAAGGAAGAACCCTCAGTGTCTCCCAGCAGCACTGGTAAAACCTATCAGCCAGGATCCTGGATG
CCACAAGATGGCAAGAGCCCCAGTAAA

Alignment

ORF - retro_cjac_3153 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGWSQDLFRFLWRSLSREVKEHVGTDQFGNKYYYIAGYKNWRGQTIREKRIVEAAKKQEVDYEPGDIPTE
          M.WSQDLFRFLWRSLSREVKEHVGTDQFGNKYYYIAGYKNWRGQTIREKRIVEAAKKQEVDYEPGDIPTE
Retrocopy MRWSQDLFRFLWRSLSREVKEHVGTDQFGNKYYYIAGYKNWRGQTIREKRIVEAAKKQEVDYEPGDIPTE

Parental  WEAWIRRTRKTPPTMEEILKNEKYREEIKIKSREFYEKEKVLSKETNEELLAPPADTQIKGHASAPYFGK
          WEAWIRRTRKTPPTMEEILKNEKYREEIKIKSREFYEKEKVLSKETNEELLAPPADTQIKGHASAPYFGK
Retrocopy WEAWIRRTRKTPPTMEEILKNEKYREEIKIKSREFYEKEKVLSKETNEELLAPPADTQIKGHASAPYFGK

Parental  EEPSVSPSSTGKTYQPGSWMPQDGKSPSK
          EEPSVSPSSTGKTYQPGSWMPQDGKSPSK
Retrocopy EEPSVSPSSTGKTYQPGSWMPQDGKSPSK

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	4.73 RPM
SRP051959_heart	0.09 RPM	10.09 RPM
SRP051959_kidney	0.09 RPM	6.26 RPM
SRP051959_liver	0.09 RPM	9.08 RPM
SRP051959_lung	0.03 RPM	4.26 RPM
SRP051959_lymph_node	0.05 RPM	3.86 RPM
SRP051959_skeletal_muscle	0.07 RPM	9.61 RPM
SRP051959_spleen	0.04 RPM	3.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3153 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013975	2 retrocopies	retro_chof_1922, retro_chof_733,
Callithrix jacchus	ENSCJAG00000015375	1 retrocopy	retro_cjac_3153 ,
Homo sapiens	ENSG00000164182	1 retrocopy	retro_hsap_2232,